"Black boxes" over content in Safari since Sierra installed (intermittent freezes, also)

Download and run Etrecheck. Copy and paste the results into your reply. Etrecheck is a diagnostic tool that was developed by one of the most respected users here in the ASC and recommended by Apple Support to provide a snapshot of the system and help identify the more obvious culprits that can adversely affect a Mac's performance.

Post a screenshot of what you're experiencing.

Hello all. Exactly as Lawrence, I'm experiencing the very same issue since I've installed macOS Sierra: sometimes there appear kinda strange black rectangles when surfing on Safari. That's very boring too.

Nobody else experience this issue too?

Do these come up when running a particular app or can it be any app including the Finder?

Post the results of running Etrecheck on your machine.

I have had the same problem when running Safari, MS Word for Mac, Adobe Reader, Firefox. Tried the EtreCheck program, here are the results.

EtreCheck version: 3.0.6 (315)

Report generated 2016-10-10 17:06:53

Download EtreCheck from https://etrecheck.com

Runtime 2:49

Performance: Excellent

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

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

Click the [Remove] links to remove adware.

Problem: Other problem

Description:

Black or white rectangles obscure the desktop or other windows open on the desktop. These cannot be removed without restarting. Very annoying.

Hardware Information: ⓘ

iMac (27-inch, Mid 2010)

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

iMac - model: iMac11,3

1 3.2 GHz Intel Core i3 CPU: 2-core

12 GB RAM Upgradeable - [Instructions]

BANK 0/DIMM0

2 GB DDR3 1333 MHz ok

BANK 1/DIMM0

2 GB DDR3 1333 MHz ok

BANK 0/DIMM1

4 GB DDR3 1333 MHz ok

BANK 1/DIMM1

4 GB DDR3 1333 MHz ok

Bluetooth: Old - Handoff/Airdrop2 not supported

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

Video Information: ⓘ

ATI Radeon HD 5670 - VRAM: 512 MB

iMac 2560 x 1440

System Software: ⓘ

macOS Sierra 10.12 (16A323) - Time since boot: about 5 hours

Disk Information: ⓘ

WDC WD1001FALS-40Y6A0 disk0 : (1 TB) (Rotational)

EFI (disk0s1) <not mounted> : 210 MB

Byron's iMac (disk0s2) / [Startup]: 999.35 GB (86.29 GB free)

Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB

HL-DT-STDVDRW GA32N ()

USB Information: ⓘ

Apple, Inc. Keyboard Hub

Apple, Inc Apple Keyboard

Apple Card Reader

Apple Inc. BRCM2046 Hub

Apple Inc. Bluetooth USB Host Controller

CP1000PFCLCD CRDA103.981

Apple Computer, Inc. IR Receiver

Apple Inc. Built-in iSight

Gatekeeper: ⓘ

Mac App Store and identified developers

Adware: ⓘ

~/Library/LaunchAgents/com.unionsoftwareonline.AppMonitor.plist

One adware file found. [Remove]

System Launch Agents: ⓘ

[not loaded] 7 Apple tasks

[loaded] 168 Apple tasks

[running] 96 Apple tasks

System Launch Daemons: ⓘ

[not loaded] 42 Apple tasks

[loaded] 161 Apple tasks

[running] 100 Apple tasks

Launch Agents: ⓘ

[loaded] com.oracle.java.Java-Updater.plist (2015-12-11) [Support]

Launch Daemons: ⓘ

[loaded] com.adobe.fpsaud.plist (2016-08-29) [Support]

[loaded] com.malwarebytes.HelperTool.plist (2016-06-28) [Support]

[loaded] com.oracle.java.Helper-Tool.plist (2015-12-11) [Support]

User Launch Agents: ⓘ

[running] com.amazon.music.plist (2016-02-12) [Support]

[loaded] com.citrixonline.GoToMeeting.G2MUpdate.plist (2016-10-07) [Support]

[running] com.spotify.webhelper.plist (2016-04-05) [Support]

[failed] com.unionsoftwareonline.AppMonitor.plist (2016-08-17) Adware! [Remove]

User Login Items: ⓘ

System Events Application (/System/Library/CoreServices/System Events.app)

AirPort Base Station Agent Application (/System/Library/CoreServices/AirPort Base Station Agent.app)

Microsoft Database Daemon Application (/Applications/Microsoft Office 2008/Office/Microsoft Database Daemon.app)

Dropbox Application (/Applications/Dropbox.app)

Internet Plug-ins: ⓘ

MeetingJoinPlugin: Unknown - SDK 10.2 (2016-04-30) [Support]

OfficeLiveBrowserPlugin: 12.3.6 (2013-03-25) [Support]

Flip4Mac WMV Plugin: 3.2.0.16 - SDK 10.8 (2013-12-03) [Support]

AdobePDFViewerNPAPI: 10.1.16 (2015-10-30) [Support]

FlashPlayer-10.6: 23.0.0.162 - SDK 10.9 (2016-10-07) [Support]

Silverlight: 5.1.50709.0 - SDK 10.6 (2016-10-04) [Support]

QuickTime Plugin: 7.7.3 (2016-09-13)

Flash Player: 23.0.0.162 - SDK 10.9 (2016-10-07) [Support]

iPhotoPhotocast: 7.0 (2010-05-06)

AdobePDFViewer: 10.1.16 (2015-10-30) [Support]

CouponPrinter-FireFox_v2: Version 1.1.6 (2011-07-27)

GarminGpsControl: 4.0.3.0 Release - SDK 10.6 (2013-10-21) [Support]

JavaAppletPlugin: Java 8 Update 101 build 13 (2016-07-25) Check version

User internet Plug-ins: ⓘ

CitrixOnlineWebDeploymentPlugin: 1.0.105 (2013-04-25) [Support]

WebEx64: 1.0 - SDK 10.10 (2015-09-30) [Support]

Safari Extensions: ⓘ

QuickBrowse - Catalin Andrei Vasiliu - http://www.unionsoftwareonline.com (2016-04-06)

3rd Party Preference Panes: ⓘ

Flash Player (2016-08-29) [Support]

Flip4Mac WMV (2013-03-29) [Support]

Java (2016-07-25) [Support]

Perian (2011-07-23) [Support]

Time Machine: ⓘ

Time Machine not configured!

Top Processes by CPU: ⓘ

13% WindowServer

5% Safari

5% AdobeReader

4% kernel_task

2% com.apple.WebKit.WebContent(12)

Top Processes by Memory: ⓘ

4.03 GB com.apple.WebKit.WebContent(12)

897 MB kernel_task

418 MB iTunes

344 MB mdworker(11)

319 MB Safari

Virtual Memory Information: ⓘ

1.90 GB Free RAM

10.00 GB Used RAM (3.23 GB Cached)

0 B Swap Used

Diagnostics Information: ⓘ

Oct 10, 2016, 03:24:23 PM ~/Library/Logs/DiagnosticReports/Mail_2016-10-10-152423_[redacted].crash

com.apple.mail - /Applications/Mail.app/Contents/MacOS/Mail

Oct 10, 2016, 01:01:51 PM ~/Library/Logs/DiagnosticReports/SystemUIServer_2016-10-10-130151_[redacted].cr ash

com.apple.systemuiserver - /System/Library/CoreServices/SystemUIServer.app/Contents/MacOS/SystemUIServer

Oct 10, 2016, 01:01:51 PM ~/Library/Logs/DiagnosticReports/UserEventAgent_2016-10-10-130151_[redacted].cr ash

/usr/libexec/UserEventAgent

Oct 10, 2016, 01:01:50 PM ~/Library/Logs/DiagnosticReports/sharingd_2016-10-10-130150_[redacted].crash

/usr/libexec/sharingd

Oct 10, 2016, 01:01:42 PM /Library/Logs/DiagnosticReports/mediaremoted_2016-10-10-130142_[redacted].crash

/System/Library/PrivateFrameworks/MediaRemote.framework/Support/mediaremoted

Oct 10, 2016, 01:01:40 PM /Library/Logs/DiagnosticReports/wifivelocityd_2016-10-10-130140_[redacted].cras h

/usr/libexec/wifivelocityd

Oct 10, 2016, 11:15:40 AM Self test - passed

Oct 8, 2016, 11:21:49 AM ~/Library/Logs/DiagnosticReports/QuickLookSatellite_2016-10-08-112149_[redacted ].crash

/System/Library/Frameworks/QuickLook.framework/Versions/A/Resources/quicklookd. app/Contents/XPCServices/QuickLookSatellite.xpc/Contents/MacOS/QuickLookSatellit e

They come up only when running Safari...

I'm posting a screenshot too, I were on Github when it appeared:

Note that I just need to go at the bottom, then I came back to the point and the black box was gone. That's very strange. Also if you select it (by inspecting the element for instance), it disappears. Never had similar issues since I've installed macOS Sierra.

Boot into Safe Mode, Mac OS X: Starting up in Safe Mode, launch Safari and see if it occurs there. If not then there's a 3rd party extension that's involved. Reboot normally and try again.

Well, it would seem they do not appear while in Safe Mode. Though I can't remember any extension which could be involved.

I mean, I've disabled all Safari extensions, and still I see those black boxes...

I suggest you boot into the Recovery volume (boot with the Command + R keys held down) and reinstall the system.

So you exclude the possibility it is related to Sierra and it might affect others?

First create a new user account and try from there. That account will not have any of the 3rd party add ons that your current account has. But will use some of the system wide launch daemons. See if the problem persists.