Q: safari keeps launching by itself

You posted it behaved in a new account. Did you try the Safe Mode?

Safe Mode - About El Capitan

Safe Mode Startup – El Capitan.

Safe mode appears to work, but it's so slow that I can't be 100% sure. I've tried eliminating some apps (MacID, TripMode, Monolingual), testing, and replacing them when the problem persists without them. I've also removed some extensions and preference panes that I probably didn't need any more (Perian, Flip4Mac, RCDefaultApp). Still the problem persists. Here's the latest from EtreCheck:

EtreCheck version: 3.0.2 (306)

Report generated 2016-08-29 10:01:59

Download EtreCheck from https://etrecheck.com

Runtime 2:01

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:

Safari relaunches

Removed various preference panes and some plug-ins

Hardware Information: ⓘ

    MacBook Pro (Retina, 15-inch, Late 2013)

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

    MacBook Pro - model: MacBookPro11,3

    1 2.3 GHz Intel Core i7 CPU: 4-core

    16 GB RAM Not upgradeable

        BANK 0/DIMM0

            8 GB DDR3 1600 MHz ok

        BANK 1/DIMM0

            8 GB DDR3 1600 MHz ok

    Bluetooth: Good - Handoff/Airdrop2 supported

    Wireless:  en0: 802.11 a/b/g/n/ac

    Battery: Health = Normal - Cycle count = 247

Video Information: ⓘ

    Intel Iris Pro

    NVIDIA GeForce GT 750M - VRAM: 2048 MB

        Color LCD 2880 x 1800

System Software: ⓘ

    OS X El Capitan 10.11.6 (15G31) - Time since boot: less than an hour

Disk Information: ⓘ

    APPLE SSD SM0512F disk0 : (500.28 GB) (Solid State - TRIM: Yes)

        EFI (disk0s1) <not mounted> : 210 MB

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

        Macintosh HD (disk1) / : 499.07 GB (63.15 GB free)

            Encrypted AES-XTS Unlocked

            Core Storage: disk0s2 499.42 GB Online

USB Information: ⓘ

    Western Digital My Passport 0820 2 TB

        EFI (disk2s1) <not mounted> : 210 MB

        John Duplicate 1 (disk2s2) /Volumes/John Duplicate 1 : 500.37 GB (69.00 GB free)

        Marjo Backup 1 (disk2s3) /Volumes/Marjo Backup 1 : 250.00 GB (50.80 GB free)

        Archive 1 (disk2s4) /Volumes/Archive 1 : 1.25 TB (124.41 GB free)

    Apple Inc. Apple Internal Keyboard / Trackpad

    Apple Inc. BRCM20702 Hub

        Apple Inc. Bluetooth USB Host Controller

    PIXART USB OPTICAL MOUSE

Thunderbolt Information: ⓘ

    Apple Inc. thunderbolt_bus

Gatekeeper: ⓘ

    Mac App Store and identified developers

Kernel Extensions: ⓘ

        /Library/Extensions

    [loaded]    at.obdev.nke.LittleSnitch (3.6.4 - SDK 10.8 - 2016-08-02) [Support]

System Launch Agents: ⓘ

    [not loaded]    8 Apple tasks

    [loaded]    160 Apple tasks

    [running]    70 Apple tasks

System Launch Daemons: ⓘ

    [not loaded]    46 Apple tasks

    [loaded]    158 Apple tasks

    [running]    87 Apple tasks

Launch Agents: ⓘ

    [running]    at.obdev.LittleSnitchUIAgent.plist (2016-08-02) [Support]

    [not loaded]    com.adobe.AAM.Updater-1.0.plist (2016-08-05) [Support]

    [loaded]    com.adobe.CS4ServiceManager.plist (2010-04-13) [Support]

    [running]    com.bjango.istatmenusagent.plist (2015-12-16) [Support]

    [running]    com.bjango.istatmenusnotifications.plist (2015-12-16) [Support]

    [running]    com.bjango.istatmenusstatus.plist (2015-12-16) [Support]

    [loaded]    com.google.keystone.agent.plist (2016-03-03) [Support]

    [loaded]    com.oracle.java.Java-Updater.plist (2014-10-25) [Support]

    [loaded]    org.macosforge.xquartz.startx.plist (2016-05-05) [Support]

Launch Daemons: ⓘ

    [running]    at.obdev.littlesnitchd.plist (2016-08-02) [Support]

    [loaded]    ch.tripmode.nke.TripMode.plist (2016-08-24)

    [running]    com.adobe.agsservice.plist (2016-08-13) [Support]

    [loaded]    com.barebones.authd.plist (2012-04-23) [Support]

    [not loaded]    com.barebones.textwrangler.plist (2011-01-14) [Support]

    [running]    com.bjango.istatmenusdaemon.plist (2015-12-16) [Support]

    [loaded]    com.charlessoft.pacifist.helper.plist (2015-12-24) [Support]

    [loaded]    com.cocoatech.pathfinder.SMFHelper7.plist (2016-06-26) [Support]

    [loaded]    com.google.keystone.daemon.plist (2016-03-03) [Support]

    [loaded]    com.microsoft.office.licensing.helper.plist (2010-08-25) [Support]

    [loaded]    com.opendoor.doorstopdaemon.plist (2010-04-13) [Support]

    [loaded]    com.oracle.java.Helper-Tool.plist (2014-10-25) [Support]

    [running]    com.stclairsoft.AppTamerAgent.plist (2015-10-15) [Support]

    [loaded]    com.stclairsoft.DefaultFolderXAgent.plist (2011-08-30) [Support]

    [loaded]    jp.co.canon.MasterInstaller.plist (2016-07-02) [Support]

    [loaded]    org.macosforge.xquartz.privileged_startx.plist (2016-05-05) [Support]

User Launch Agents: ⓘ

    [loaded]    com.adobe.AAM.Updater-1.0.plist (2016-06-22) [Support]

    [not loaded]    com.linotype.FontFolderProtector.plist (2016-08-29) [Support]

User Login Items: ⓘ

    Flux    Application  (/Applications/Flux.app)

    Watts    Application  (/Applications/Utilities 3rd Party/Interface Utilities/Watts.app)

    Dashboard KickStart    Application  (/Library/PreferencePanes/Dashboard KickStart.prefPane/Contents/Resources/Dashboard KickStart.app)

    LaunchBar    Application  (/Applications/Utilities 3rd Party/Interface Utilities/LaunchBar.app)

    Path Finder    Application  (/Applications/Utilities 3rd Party/Interface Utilities/Path Finder.app)

    FontExplorer X Pro    Application Hidden (/Applications/FontExplorer X Pro.app)

    Typinator    Application  (/Applications/Typinator.app)

    App Tamer    Application Hidden (/Applications/App Tamer.app)

    Canon IJ Network Scanner Selector EX    Application Hidden (/Applications/Canon Utilities/IJ Network Scanner Selector EX/Canon IJ Network Scanner Selector EX.app)

    Dropbox    Application  (/Applications/Dropbox.app)

    PopChar    Application  (/Applications/PopChar.app)

    Default Folder X    Application  (/Applications/Default Folder X.app)

    Synergy    Application  (/Applications/Utilities 3rd Party/Interface Utilities/Synergy/Synergy Preferences.app/Contents/PreferencePanes/Synergy.prefPane/Contents/Helpers/Syne rgy.app)

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

    DragThing    Application  (/Applications/Utilities 3rd Party/Interface Utilities/DragThing.app)

    MacID    Application  (/Applications/MacID.app)

Internet Plug-ins: ⓘ

    AdobeAAMDetect: AdobeAAMDetect 1.0.0.0 - SDK 10.6 (2015-10-07) [Support]

    JavaAppletPlugin: Java 8 Update 102 build 14 (2016-08-24) Check version

    QuickTime Plugin: 7.7.3 (2016-08-03)

    AdobePDFViewerNPAPI: 11.0.17 - SDK 10.6 (2016-08-02) [Support]

    AdobePDFViewer: 11.0.17 - SDK 10.6 (2016-08-02) [Support]

    Default Browser: 601 - SDK 10.11 (2016-08-03)

    SharePointBrowserPlugin: 14.6.7 - SDK 10.6 (2016-08-23) [Support]

    Google Earth Web Plug-in: 7.1 (2016-08-20) [Support]

    npViewpoint: 1.0 (2011-07-15)

    iPhotoPhotocast: 7.0 (2010-04-14)

User internet Plug-ins: ⓘ

    Folx3Plugin: 4.0 - SDK 10.6 (2015-07-26) [Support]

    AddLive_v3: AddLive_v3 3.0.6.3 (2016-04-13) [Support]

    Google Earth Web Plug-in: 7.1 (2013-10-08) [Support]

Audio Plug-ins: ⓘ

    iWow: Unknown (2011-09-28) [Support]

3rd Party Preference Panes: ⓘ

    Dashboard KickStart (2014-01-09) [Support]

    Java (2016-06-22) [Support]

    TeXDistPrefPane (2010-05-10) [Support]

Time Machine: ⓘ

    Skip System Files: NO

    Mobile backups: ON

    Auto backup: YES

    Volumes being backed up:

        Macintosh HD: Disk size: 499.07 GB Disk used: 435.91 GB

    Destinations:

        Archive 1 [Local]

        Total size: 1.25 TB

        Total number of backups: 54

        Oldest backup: 5/10/2015, 7:35

        Last backup: 29/08/2016, 8:59

        Size of backup disk: Too small

            Backup size 1.25 TB < (Disk used 435.91 GB X 3)

        Data [Network]

        Total size: 2.00 TB

        Total number of backups: 70

        Oldest backup: 4/04/2015, 2:08

        Last backup: 29/08/2016, 8:06

        Size of backup disk: Excellent

            Backup size 2.00 TB > (Disk size 499.07 GB X 3)

Top Processes by CPU: ⓘ

         2%    fontd

         2%    App Tamer

         2%    WindowServer

         1%    iStat Menus Status

         1%    kernel_task

Top Processes by Memory: ⓘ

    1.19 GB    kernel_task

    999 MB    Google Chrome Helper(11)

    770 MB    LaunchBar

    541 MB    mdworker(24)

    442 MB    mds_stores

Virtual Memory Information: ⓘ

    7.81 GB    Free RAM

    8.18 GB    Used RAM (2.55 GB Cached)

    0 B    Swap Used

Diagnostics Information: ⓘ

    Aug 29, 2016, 09:50:05 AM    Self test - passed

I don't see anything. The following is a guess. Go to AppTamer and set it so it ignores Safari.