Missing preferences icons from Apple menu

Question

Missing preferences icons from Apple menu

I have a late 2013 27" iMac 3.5GHz I7 with 3tb Fusion drive running OS X 10.11.4

When I try to open my system preferences from the Apple menu dropdown all I get is an empty box named System Preferences and the icon in the dock looks like a text file icon.

If I right click on the icon in my dock while the empty box is open I can click on whatever it is that I am wanting to do.

Now, if I open the system preferences from within the applications folder in finder it all opens and looks as it should with no issues at all…

I’m stumped…

I tried repairing the permissions but that didn’t help.

iMac (27-inch, Late 2013)

Posted on Apr 16, 2016 4:31 PM

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Answer 1

Linc Davis

Level 10

209,739 points

Apr 16, 2016 5:38 PM in response to iMacfrombluff city

Please read this whole message before doing anything.

This procedure is a test, not a solution. Don’t be disappointed when you find that nothing has changed after you complete it.

Step 1

The purpose of this step is to determine whether the problem is localized to your user account.

Enable guest logins* and log in as Guest. Don't use the Safari-only “Guest User” login created by “Find My Mac.”

While logged in as Guest, you won’t have access to any of your documents or settings. Applications will behave as if you were running them for the first time. Don’t be alarmed by this behavior; it’s normal. If you need any passwords or other personal data in order to complete the test, memorize, print, or write them down before you begin.

Test while logged in as Guest. Same problem?

After testing, log out of the guest account and, in your own account, disable it if you wish. Any files you created in the guest account will be deleted automatically when you log out of it.

*Note: If you’ve activated “Find My Mac” or FileVault, then you can’t enable the Guest account. The “Guest User” login created by “Find My Mac” is not the same. Create a new account in which to test, and delete it, including its home folder, after testing.

Step 2

The purpose of this step is to determine whether the problem is caused by third-party system modifications that load automatically at startup or login, by a peripheral device, by a font conflict, or by corruption of the file system or of certain system caches.

Please take this step regardless of the results of Step 1.

Disconnect all wired peripherals except those needed for the test, and remove all aftermarket expansion cards, if applicable. Start up in safe mode and log in to the account with the problem.

Note: If FileVault is enabled in OS X 10.9 or earlier, or if a firmware password is set, or if the startup volume is a software RAID, you can’t do this. Ask for further instructions.

Safe mode is much slower to start up and run than normal, with limited graphics performance, and some things won’t work at all, including sound output and Wi-Fi on certain models. The next normal startup may also be somewhat slow.

The login screen appears even if you usually log in automatically. You must know your login password in order to log in. If you’ve forgotten the password, you will need to reset it before you begin.

Test while in safe mode. Same problem?

After testing, restart as usual (not in safe mode) and verify that you still have the problem. Post the results of Steps 1 and 2.

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Answer 2

Apr 16, 2016 7:23 PM in response to Linc Davis

Ok, interesting!

Step one results, system prefs from the Apple menu are there as they should be.

Step two results. same as above.

My one peripheral that seems to be causing this issue is my OWC Thunderbay box which connects via a Thunderbolt cable.

Not sure if there is a fix for this as my Thunderbay box must be online...maybe contacting OWC could help, unless you have a suggestion??

Thank you very much for the help!

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Answer 3

Linc Davis

Level 10

209,739 points

Apr 16, 2016 7:35 PM in response to iMacfrombluff city

Step two results. same as above.

Same as Step 1, or same as when you started?

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Answer 4

Apr 16, 2016 7:50 PM in response to Linc Davis

I'm sorry, same as step 1.

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Answer 5

Linc Davis

Level 10

209,739 points

Apr 16, 2016 8:17 PM in response to iMacfrombluff city

And when you restart as usual?

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Answer 6

Apr 19, 2016 2:42 PM in response to Linc Davis

No change after a restart.

I have an OWC Extreme 6g 1TB in the Thunderbay box that I use to Carbon Copy clone the internal fusion, when I boot from this clone (updated every day @ 3AM) everything is normal...

If I boot from the internal 3TB fusion I get the missing icons in the Apple Menu system prefs link...

This doesn't help my confusion...but if I boot from the external thunderbolt SSD life is good!

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Answer 7

Apr 19, 2016 2:43 PM in response to iMacfrombluff city

Thanks for your help. Although it's still a mystery to me, I can live with it as it is.

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Answer 8

Eric Root

Level 10

685,311 points

Apr 19, 2016 4:17 PM in response to iMacfrombluff city

Try running this program and then copy and paste the output in a reply. The program was created by Etresoft, a frequent contributor. Please use copy and paste as screen shots can be hard to read.

Etrecheck – System Information

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Answer 9

Apr 27, 2016 3:24 PM in response to Eric Root

Sorry to take so long to come back to this..

Here's the report:

EtreCheck version: 2.9.11 (264)

Report generated 2016-04-27 18:19:53

Download EtreCheck from https://etrecheck.com

Runtime 2:29

Performance: Excellent

Click the [Support] links for help with non-Apple products.

Click the [Details] links for more information about that line.

Problem: Other problem

Description:

Missing icons from the System Prefs pane

Hardware Information:ⓘ

iMac (27-inch, Late 2013)

[Technical Specifications] - [User Guide] - [Warranty & Service]

iMac - model: iMac14,2

1 3.5 GHz Intel Core i7 CPU: 4-core

32 GB RAM Upgradeable - [Instructions]

BANK 0/DIMM0

8 GB DDR3 1600 MHz ok

BANK 1/DIMM0

8 GB DDR3 1600 MHz ok

BANK 0/DIMM1

8 GB DDR3 1600 MHz ok

BANK 1/DIMM1

8 GB DDR3 1600 MHz ok

Bluetooth: Good - Handoff/Airdrop2 supported

Wireless: en1: 802.11 a/b/g/n/ac

Video Information:ⓘ

NVIDIA GeForce GTX 780M - VRAM: 4096 MB

iMac 2560 x 1440

System Software:ⓘ

OS X El Capitan 10.11.4 (15E65) - Time since boot: about one day

Disk Information:ⓘ

APPLE SSD SD0128F disk0 : (121.33 GB) (Solid State - TRIM: Yes)

EFI (disk0s1) <not mounted> : 210 MB

Boot OS X (disk0s3) <not mounted> : 134 MB

Macintosh HD (disk2) /Volumes/Macintosh HD : 3.11 TB (2.46 TB free)

Core Storage: disk0s2 120.99 GB Online

Core Storage: disk1s2 3.00 TB Online

APPLE HDD ST3000DM001 disk1 : (3 TB) (Rotational)

EFI (disk1s1) <not mounted> : 210 MB

Recovery HD (disk1s3) <not mounted> [Recovery]: 650 MB

Macintosh HD (disk2) /Volumes/Macintosh HD : 3.11 TB (2.46 TB free)

Core Storage: disk0s2 120.99 GB Online

Core Storage: disk1s2 3.00 TB Online

OWC Mercury EXTREME Pro 6G SSD disk3 : (960.2 GB) (Solid State - TRIM: No)

EFI (disk3s1) <not mounted> : 210 MB

iMac SSD (disk3s2) / : 959.20 GB (331.27 GB free)

Recovery HD (disk3s3) <not mounted> [Recovery]: 650 MB

ST3000DM001-1ER166 disk6 : (3 TB) (Rotational)

EFI (disk6s1) <not mounted> : 210 MB

Plex (disk6s2) /Volumes/Plex : 3.00 TB (564.65 GB free)

ST3000DM001-1ER166 disk5 : (3 TB) (Rotational)

EFI (disk5s1) <not mounted> : 210 MB

Plex Backup (disk5s2) /Volumes/Plex Backup : 3.00 TB (545.67 GB free)

ST3000DM003-1F216N disk4 : (3 TB) (Rotational)

EFI (disk4s1) <not mounted> : 210 MB

Storage (disk4s2) /Volumes/Storage : 3.00 TB (1.80 TB free)

USB Information:ⓘ

VIA Labs, Inc. USB3.0 Hub

Apple Inc. BRCM20702 Hub

Apple Inc. Bluetooth USB Host Controller

Apple Inc. FaceTime HD Camera (Built-in)

Apple, Inc. Keyboard Hub

Logitech USB Receiver

Apple Inc. Apple Keyboard

VIA Labs, Inc. USB2.0 Hub

Thunderbolt Information:ⓘ

Apple Inc. thunderbolt_bus

Other World Computing ThunderBay 4

Gatekeeper:ⓘ

Anywhere

Kernel Extensions:ⓘ

/Library/Extensions

[loaded] at.obdev.nke.LittleSnitch (3.6.2 - SDK 10.8 - 2016-04-15) [Support]

[loaded] com.Logitech.Control Center.HID Driver (3.9.1 - SDK 10.8 - 2016-04-15) [Support]

[loaded] com.Logitech.Unifying.HID Driver (1.3.1 - SDK 10.8 - 2016-04-15) [Support]

[loaded] com.paragon-software.filesystems.ntfs (14.0.543 - SDK 10.5 - 2016-04-15) [Support]

[loaded] com.paragon-software.kext.VDMounter (602.2 - SDK 10.8 - 2016-04-15) [Support]

/Volumes/Macintosh HD/Applications/ESET Cyber Security.app

[loaded] com.eset.kext.esets-kac (6.1.12 - SDK 10.6 - 2016-01-22) [Support]

[not loaded] com.eset.kext.esets-mac (6.1.12 - SDK 10.6 - 2016-01-22) [Support]

[loaded] com.eset.kext.esets-pfw (6.1.12 - SDK 10.6 - 2016-01-22) [Support]

/Volumes/Macintosh HD/Applications/Parallels Desktop.app

[not loaded] com.parallels.kext.hypervisor (10.2.1 29006 - SDK 10.7 - 2016-04-06) [Support]

[not loaded] com.parallels.kext.netbridge (10.2.1 29006 - SDK 10.7 - 2016-04-06) [Support]

[not loaded] com.parallels.kext.usbconnect (10.2.1 29006 - SDK 10.7 - 2016-04-06) [Support]

[not loaded] com.parallels.kext.vnic (10.2.1 29006 - SDK 10.7 - 2016-04-06) [Support]

/Volumes/Macintosh HD/Applications/Toast 14 Titanium/Toast Audio Assistant.app

[not loaded] com.Cycling74.driver.Soundflower (1.6.7 - SDK 10.7 - 2016-01-04) [Support]

/Volumes/Macintosh HD/Users/[redacted]/Library/Services/ToastIt.service/Contents/MacOS

[not loaded] com.roxio.TDIXController (2.0 - 2015-12-31) [Support]

Startup Items:ⓘ

TuxeraNTFSUnmountHelper: Path: /Library/StartupItems/TuxeraNTFSUnmountHelper

Startup items are obsolete in OS X Yosemite

System Launch Agents:ⓘ

[not loaded] 7 Apple tasks

[loaded] 154 Apple tasks

[running] 77 Apple tasks

System Launch Daemons:ⓘ

[not loaded] 45 Apple tasks

[loaded] 156 Apple tasks

[running] 87 Apple tasks

Launch Agents:ⓘ

[running] at.obdev.LittleSnitchUIAgent.plist (2016-01-28) [Support]

[running] com.Logitech.Control Center.Daemon.plist (2015-09-18) [Support]

[loaded] com.epson.esua.launcher.plist (2016-03-28) [Support]

[running] com.epson.eventmanager.agent.plist (2012-05-08) [Support]

[loaded] com.google.keystone.agent.plist (2016-04-10) [Support]

[not loaded] com.maintain.LogOut.plist (2015-12-24) [Support]

[not loaded] com.maintain.PurgeInactiveMemory.plist (2015-12-24) [Support]

[not loaded] com.maintain.Restart.plist (2015-12-24) [Support]

[not loaded] com.maintain.ShutDown.plist (2015-12-24) [Support]

[not loaded] com.maintain.Sleep.plist (2015-12-24) [Support]

[running] com.maintain.SystemEvents.plist (2015-12-24) [Support]

[running] com.paragon-software.NTFS.fsnotifyagent.plist (2015-10-25) [Support]

[loaded] com.paragon.updater.plist (2015-10-25) [Support]

[running] com.softraid.SoftRAIDMonitor.plist (2016-04-15) [Support]

[running] org.gpgtools.Libmacgpg.xpc.plist (2015-09-23) [Support]

[loaded] org.gpgtools.gpgmail.enable-bundles.plist (2015-03-08) [Support]

[loaded] org.gpgtools.gpgmail.patch-uuid-user.plist (2015-03-08) [Support]

[loaded] org.gpgtools.gpgmail.updater.plist (2015-09-23) [Support]

[loaded] org.gpgtools.macgpg2.fix.plist (2015-03-08) [Support]

[running] org.gpgtools.macgpg2.shutdown-gpg-agent.plist (2015-03-08) [Support]

[loaded] org.gpgtools.macgpg2.updater.plist (2015-03-08) [Support]

[loaded] org.macosforge.xquartz.startx.plist (2015-10-16) [Support]

Launch Daemons:ⓘ

[running] at.obdev.littlesnitchd.plist (2016-01-28) [Support]

[loaded] com.adobe.fpsaud.plist (2016-01-29) [Support]

[running] com.bombich.ccchelper.plist (2015-12-27) [Support]

[loaded] com.bresink.system.privilegedhelper-tts.plist (2016-04-06) [Support]

[running] com.eset.esets_daemon.plist (2015-09-25) [Support]

[loaded] com.google.keystone.daemon.plist (2016-04-10) [Support]

[not loaded] com.maintain.CocktailScheduler.plist (2015-12-24) [Support]

[not loaded] com.maintain.HideSpotlightMenuBarIcon.plist (2015-12-24) [Support]

[loaded] com.malwarebytes.MBAMHelperTool.plist (2016-01-05) [Support]

[loaded] com.paragon-software.installer.plist (2016-03-25) [Support]

[loaded] com.paragon-software.vdmounter.plist (2016-02-05) [Support]

[loaded] com.paragon.NTFS.launch.plist (2015-10-25) [Support]

[running] com.softraid.softraidd.plist (2016-04-15) [Support]

[running] com.tunabellysoftware.TGFanHelper.plist (2015-12-23) [Support]

[loaded] org.gpgtools.gpgmail.patch-uuid.plist (2015-03-08) [Support]

[loaded] org.macosforge.xquartz.privileged_startx.plist (2015-10-16) [Support]

User Launch Agents:ⓘ

[loaded] com.bittorrent.uTorrent.plist (2016-04-19) [Support]

[loaded] com.koingosw.MacCleanse4Helper.Reminder.plist (2016-04-26) [Support]

[loaded] com.koingosw.MacCleanse4Helper.TrashWatcher.plist (2016-04-26) [Support]

[loaded] com.pia.pia_manager.plist (2015-12-23) [Support]

[loaded] com.valvesoftware.steamclean.plist (2016-04-27) [Support]

User Login Items:ⓘ

VoilaHelper Application (/Applications/Voila.app/Contents/Library/LoginItems/VoilaHelper.app)

iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)

Plex Media Server Application (/Applications/Plex Media Server.app)

CCC User Agent Application (/Applications/Carbon Copy Cloner.app/Contents/Library/LoginItems/CCC User Agent.app)

Android File Transfer Agent Application (~/Library/Application Support/Google/Android File Transfer/Android File Transfer Agent.app)

HyperDock Helper Application (/Applications/HyperDock.app/Contents/Library/LoginItems/HyperDock Helper.app)

ESET Cyber Security Application (/Applications/ESET Cyber Security.app)

Other Apps:ⓘ

[running] com.bombich.cccuseragent.56352

[running] com.coppertino.VOXAgent

[running] com.eset.ecs.6.612192

[running] com.eset.ecs.6.63712

[running] com.etresoft.EtreCheck.704032

[running] com.globaldelight.VoilaCapture.239072

[running] com.google.Chrome.307552

[running] com.google.android.mtpagent.12512

[running] com.plexapp.plexmediaserver.88032

[loaded] com.trendmicro.ATLoginItemHelper

[running] com.trendmicro.DrCleaner.59232

[loaded] com.tunabellysoftware.TGProLaunchHelper

[running] com.tunabellysoftware.tgpro.96032

[running] com.valvesoftware.steam.ipctool

[running] de.bahoom.HyperDock-Helper.76512

[running] net.freemacsoft.AppCleaner-SmartDelete

[loaded] 420 Apple tasks

[running] 213 Apple tasks

Internet Plug-ins:ⓘ

Flip4Mac WMV Plugin: 2.3.5.4 (2010-09-10) [Support]

FlashPlayer-10.6: 20.0.0.306 - SDK 10.6 (2016-02-14) [Support]

QuickTime Plugin: 7.7.3 (2016-04-10)

Flash Player: 20.0.0.306 - SDK 10.6 (2016-02-14) Outdated! Update

Default Browser: 601 - SDK 10.11 (2016-04-10)

PepperFlashPlayer: 20.0.0.267 - SDK 10.6 (2016-01-16) [Support]

Silverlight: 4.0.50826.0 (2016-01-30) [Support]

Safari Extensions:ⓘ

AdBlock - BetaFish, Inc. - https://getadblock.com (2015-12-26)

Open in Internet Explorer - Parallels - http://www.parallels.com (2016-02-06)

Adblock Plus - Eyeo GmbH - https://adblockplus.org/ (2016-01-10)

Aimersoft Video Converter - Aimersoft Studio - http://www.aimersoft.com (2013-10-14)

3rd Party Preference Panes:ⓘ

Flash Player (2016-01-29) [Support]

GPGPreferences (2016-03-12) [Support]

Logitech Control Center (2016-04-06) [Support]

Paragon NTFS for Mac ® OS X (2016-04-06) [Support]

Time Machine:ⓘ

Skip System Files: NO

Mobile backups: OFF

Auto backup: NO - Auto backup turned off

Volumes being backed up:

Macintosh HD: Disk size: 3.11 TB Disk used: 650.68 GB

Storage: Disk size: 3.00 TB Disk used: 1.20 TB

Destinations:

Time Machine Drive [Local]

Total size: 3.00 TB

Total number of backups: 21

Oldest backup: 12/25/15, 8:35 AM

Last backup: 12/27/15, 11:04 AM

Size of backup disk: Too small

Backup size 3.00 TB < (Disk used 1.85 TB X 3)

Top Processes by CPU:ⓘ

3% WindowServer

2% fontd

1% esets_daemon(2)

1% Google Chrome

1% kernel_task

Top Processes by Memory:ⓘ

1.51 GB kernel_task

950 MB Google Chrome Helper(7)

459 MB softwareupdated

197 MB mds_stores

164 MB Plex Media Server

Virtual Memory Information:ⓘ

24.00 GB Free RAM

7.59 GB Used RAM (2.37 GB Cached)

0 B Swap Used

Diagnostics Information:ⓘ

Apr 26, 2016, 07:24:03 PM Self test - passed

Apr 26, 2016, 06:05:47 PM /Library/Logs/DiagnosticReports/esets_proxy_2016-04-26-180547_[redacted].crash

/Applications/ESET Cyber Security.app/Contents/MacOS/esets_proxy

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Answer 10

Apr 27, 2016 4:28 PM in response to iMacfrombluff city

I have since enables Trim for the external boot SSD

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