Safari 5.1.2 having identity crisis?

Question

Hello all,
I have been using Safari 5.1.2 since its release. This afternoon I ran into a bizarre issue which I simply cannot resolve.
Here is what happened:
Roughly ten hours ago I launched Safari to check my university email. In order to do so, I opened the preferences pane and enabled Java Script. Upon finishing, I disabled JavaScript, cleared out cookies & flash cookies, reset Safari, and closed it. (I do this every time I use Safari, without incident). When I was in the preferences pane, all was in order: my extensions were in place & working, ditto Safari Cookies, etc. Business as usual.
Approximately five hours thereafter I launched Safari to search for an article on the web. After completing my search, I opened the preferences pane only to discover that my extensions were disabled, and "Safari Cookies" was gone. Under the "extensions" tab I selected "get extensions", and was duly informed that in order to use Safari extensions I must update to Safari 5. Checking "About Safari" showed that I was running 5.1.2.
Over the past few hours I cleared my history and cache & restarted Safari. The issue remained. I then reset Safari. That did not work either. Subsequently I restarted my MacBook; uninstalled Safari Cookies (since it was disabled anyway); manually removed caches, pref files, logs, localizations, binaries, etc. (just to be thorough); and ran Onyx. I then restarted…
Nope. My extensions remain disabled, I cannot reinstall Safari Cookies, and Safari 5.1.2 continues to insist that I update to Safari 5.
Short of uninstalling Safari itself, cleaning everything out again, and reinstalling Safari, I am at a loss as to how to address this issue. Any suggestions would be greatly appreciated.
sjl
13" aluminum MacBook
2.4 GHz, 4 GB
Mac OS X (10.7.2)

Answer 1

Thank you for the incredibly prompt response.
Step 1 :
com.rogueamoeba.HermesAudio(3.0.1)
com.Cycling74.driver.Soundflower(1.5.1)
com.eltima.ElmediaPlayer.kext(1.0)
Step 2 :
Password:
com.vmware.launchd.vmware
com.rogueamoeba.hermes
com.nano8blazex.NanoCustomizer
com.machangout.glims.loader
com.intego.BackupAssistant.daemon
com.eltima.ElmediaPlayer.daemon
com.bombich.ccc
Step 3 :
net.culater.SIMBL.Agent
com.intego.backupassistant.agent
com.brother.LOGINserver
com.adobe.CS4ServiceManager
com.adobe.ARM.925793fb327152fd34795896fa1fb9ffa268b2a852256fe56609efa3
Step 4 :
/Library/Components:
/Library/Extensions:
/Library/Frameworks:
AEProfiling.framework
AERegistration.framework
Adobe AIR.framework
Appscript.framework
AudioMixEngine.framework
DRS_DPE.framework
EWSMac-GC.framework
EWSMac.framework
Format_DPE.framework
GlimsAdditions.framework
HPDeviceModel.framework
HPSmartPrint.framework
MacFUSE.framework
NyxAudioAnalysis.framework
PluginManager.framework
Python.framework
TSLicense.framework
swift.framework
/Library/Input Methods:
/Library/Internet Plug-Ins:
AdobePDFViewer.plugin
DirectorShockwave.plugin
Disabled Plug-Ins
Flash Player.plugin
GlimsAdditions.webplugin
JavaAppletPlugin.plugin
NPDjVu.plugin
PangeaVR.bundle
Quartz Composer.webplugin
QuickTime Plugin.plugin
RealPlayer Plugin.plugin
Silverlight.plugin
flashplayer.xpt
googletalkbrowserplugin.plugin
iPhotoPhotocast.plugin
npgtpo3dautoplugin.plugin
nsIQTScriptablePlugin.xpt
/Library/LaunchAgents:
com.adobe.CS4ServiceManager.plist
com.brother.LOGINserver.plist
com.intego.backupassistant.agent.plist
com.machangout.glims.agent.plist
/Library/LaunchDaemons:
com.apple.remotepairtool.plist
com.bombich.ccc.plist
com.eltima.ElmediaPlayer.daemon.plist
com.intego.BackupAssistant.daemon.plist
com.machangout.glims.loader.plist
com.nano8blazex.NanoCustomizer.plist
com.rogueamoeba.hermes.plist
com.vmware.launchd.vmware.plist
/Library/PreferencePanes:
Bluetoggle.prefPane
CepstralVoices.prefPane
Flash Player.prefPane
Growl.prefPane
Jitouch.prefPane
Spelling.prefPane
TeXDistPrefPane.prefPane
/Library/PrivilegedHelperTools:
com.bombich.ccc
com.nano8blazex.NanoCustomizer
/Library/QuickLook:
GBQLGenerator.qlgenerator
VMware Fusion QuickLook.qlgenerator
iWork.qlgenerator
/Library/QuickTime:
AppleIntermediateCodec.component
AppleMPEG2Codec.component
CanonMJPEGAVI.component
CanonMJPEGAVIDec.component
CanonText.component
Google Camera Adapter 0.component
Google Camera Adapter 1.component
/Library/ScriptingAdditions:
.DS_Store
Adobe Unit Types.osax
Glims.osax
/Library/StartupItems:
Intego Backup Assistant
Library/Address Book Plug-Ins:
SkypeABDialer.bundle
SkypeABSMS.bundle
Library/Frameworks:
EWSMac.framework
Library/Input Methods:
.localized
Library/Internet Plug-Ins:
GlimsAddition.notplugin
Library/LaunchAgents:
com.adobe.ARM.925793fb327152fd34795896fa1fb9ffa268b2a852256fe56609efa3.plist
[email protected]
Library/PreferencePanes:
BlueHarvest.prefPane
Jitouch.prefPane
Perian.prefPane
Library/QuickTime:
AC3MovieImport.component
Perian.component
Library/Services:
cocoAspell.service
Hmm… Some of the following is off-topic; nonetheless…
Two years ago I downloaded ElmediaPlayer, & then uninstalled it the same day. Be that as it may, I've been endlessly deleting pieces of it ever since. A similar state of affairs prevails for Skype, VMWare Fusion, DjVu, PangeaVR, Real Player, Intego backup assistant, & GoogleTalk browser plugin.
More on-topic, I honestly believed that I had managed to rid myself off all the odds & ends of SIMBL this afternoon; apparently not. Interesting, albeit not surprising.
Any thoughts/suggestions?