Frequent freezes since update to 10.6.8

Hi all,
Thanks for you help in advance
I updated to 10.6.8 and first had a problem with the dock using 100% CPU, I worked around this using the fix provided here http://bit.ly/mPCVii
The thing is, I have nother problem now, every once and a while (20 minutes, 40 minutes, etc ...) one app hangs, so I switch to a new app or go to the dock or try to force quit it and the whole computer freezes for 20-30 seconds and then eveyrthing comes back to normal.
This happens whether I've got 1 or 10 apps launched and it also happens whether I'm on a simple app like TextEdit, Chrome or Safari or more powerful ones like Parallels, Photoshop, etc ... which makes me beleive that this isn't an app oriented issue.
Also, after the update to 10.6.8 and after the Airport Update, I had to repair permissions for these, they all got repaired using disk utility except for one which is the remote desktop agent (ARDagent), myabe this is linked sonce there was a security issue in Leopard 2 years ago with this.
I've also tried resetting PRAM and rebooting in Safe Mode.
Thanks for your help gents.
Kind Regards,
Arnaud
MacBook Pro 2011 15'
2 GHz Intel Core i7
8Gb RAM
512Gb crucial SSD

Arnaud,
     I am also experiencing the frequent freezes and the 100% CPU usage since the upgrade. I looked online and fixed the CPU usage with the fix mentioned in the thread but still have the freezes.
     I just verified my permissions and i had a bunch issues. I repaired them and now they're reporting ok. I'm going to try resetting SMC and I hope that takes care of it.
     I read your comment about the SATA II drives and i wanted to let you know i don't think it's that. I had two SATA 2 drives in my macbook and upgraded to 2 SATA 3 drives two days ago. I thought the freezes were related to one of my drives but now i not sure. I don't remember having any problems with my old SSDs but then again i can't remember if i upgraded to 10.6.8 when i had those in my system. I guess what i'm saying is that it appears the problem occurs regardless of if you have SATA 2 or SATA 3 SSDs in the system.
     Something that i found odd was some of my xbench scores. Before i fixed the CPU problem i received about a 600 for my SSDs. Right after i fixed it went down to about 440. I did the permission fix and it went back up to 500 then right back down to 440s. I don't know if that has anything to do with the upgrade but it's definitely odd...
     I'm half tempted to reinstall OSX not upgrade to 10.6.8. I could see that stops the freezes stop and if the Xbench results go back to the 600s....  If not, Lions only a week away. Maybe that will fix everything. Hopefully someone has some suggestions. If i decide to reinstall ill post my findings.

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              [loaded] com.wyse.MacCompanion.plist 3rd-Party support link
              [loaded] net.culater.SIMBL.Agent.plist 3rd-Party support link
    User Launch Agents:
              [loaded] com.adobe.AAM.Updater-1.0.plist 3rd-Party support link
              [loaded] com.adobe.ARM.[...].plist 3rd-Party support link
              [loaded] com.logos.LogosIndexer.plist 3rd-Party support link
              [loaded] com.macpaw.CleanMyMac.helperTool.plist 3rd-Party support link
              [loaded] com.macpaw.CleanMyMac.trashSizeWatcher.plist 3rd-Party support link
              [loaded] com.macpaw.CleanMyMac.volumeWatcher.plist 3rd-Party support link
    User Login Items:
              GrowlHelperApp
              iTunesHelper
              Microsoft Database Daemon
              VMware Fusion Helper
              VMware Fusion Start Menu
              Dropbox
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              SPanel
              HP Product Research
    Internet Plug-ins:
              hpvirtualrooms-plugin: Version: (null)
              o1dbrowserplugin: Version: 5.1.2.17113 3rd-Party support link
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              AdobePDFViewerNPAPI: Version: 10.1.8 3rd-Party support link
              FlashPlayer-10.6: Version: 11.9.900.170 - SDK 10.6 3rd-Party support link
              Silverlight: Version: 5.1.10411.0 - SDK 10.6 3rd-Party support link
              Flash Player: Version: 11.9.900.170 - SDK 10.6 Outdated! Update
              iPhotoPhotocast: Version: 7.0 - SDK 10.8
              CitrixICAClientPlugIn: Version: 1.0 - SDK 10.6 3rd-Party support link
              npgtpo3dautoplugin: Version: 0.1.44.29 - SDK 10.5 3rd-Party support link
              AdobePDFViewer: Version: 10.1.8 3rd-Party support link
              GarminGpsControl: Version: 4.0.1.0 Release - SDK 10.6 3rd-Party support link
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              AppleAVBAudio: Version: 2.0.0 - SDK 10.9
              iSightAudio: Version: 7.7.3 - SDK 10.9
    User Internet Plug-ins:
              WebEx64: Version: 1.0 - SDK 10.5 3rd-Party support link
    3rd Party Preference Panes:
              Citrix ShareFile Sync  3rd-Party support link
              Flash Player  3rd-Party support link
              Growl  3rd-Party support link
    Bad Fonts:
              None
    Old Applications:
              /Library/Application Support/Microsoft/MERP2.0
                        Microsoft Error Reporting:          Version: 2.2.9 - SDK 10.4 3rd-Party support link
                        Microsoft Ship Asserts:          Version: 1.1.4 - SDK 10.4 3rd-Party support link
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                        /Applications/Microsoft Office 2011/Office/Add-Ins/Solver.app
              CameraWindow:          Version: 7.10.1.3 - SDK 10.5 3rd-Party support link
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              SLLauncher:          Version: 1.0 - SDK 10.5 3rd-Party support link
                        /Library/Application Support/Microsoft/Silverlight/OutOfBrowser/SLLauncher.app
              /Applications/Microsoft Office 2011/Office
                        Microsoft Graph:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Database Utility:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Office Reminders:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Upload Center:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        My Day:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        SyncServicesAgent:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Open XML for Excel:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Alerts Daemon:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Database Daemon:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Chart Converter:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Clip Gallery:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
              /Applications/Microsoft Office 2011
                        Microsoft PowerPoint:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Excel:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Outlook:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Word:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        Microsoft Document Connection:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
              Microsoft Language Register:          Version: 14.3.9 - SDK 10.5 3rd-Party support link
                        /Applications/Microsoft Office 2011/Additional Tools/Microsoft Language Register/Microsoft Language Register.app
              WebEx Player:          Version: 8.0.0 - SDK 10.5 3rd-Party support link
                        /Users/[redacted]/Library/Application Support/WebEx Folder/1224/WebEx Player.app
              Aimersoft Helper Compact:          Version: 2.2.5.6 - SDK 10.5 3rd-Party support link
                        /Users/[redacted]/Library/Application Support/Helper/Aimersoft Helper Compact.app
              Microsoft AutoUpdate:          Version: 2.3.6 - SDK 10.4 3rd-Party support link
                        /Library/Application Support/Microsoft/MAU2.0/Microsoft AutoUpdate.app
              Garmin WebUpdater:          Version: 2.1.3 - SDK 10.4 3rd-Party support link
              Aimersoft Video Converter Ultimate:          Version: 1.6.2 - SDK 10.5 3rd-Party support link
              OmniFocus:          Version: 1.9.4 - SDK 10.4 3rd-Party support link
    Time Machine:
              Skip System Files: NO
              Auto backup: YES
              Volumes being backed up:
                        Macintosh HD: Disk size: 930.71 GB Disk used: 427.23 GB
              Destinations:
                        CalDigit AV Driev [Local] (Last used)
                        Total size: 2 
                        Total number of backups: 81
                        Oldest backup: 2012-07-16 23:44:31 +0000
                        Last backup: 2014-01-21 22:19:30 +0000
                        Size of backup disk: Adequate
                                  Backup size 2  > (Disk used 427.23 GB X 3)
              Time Machine details may not be accurate.
              All volumes being backed up may not be listed.
    Top Processes by CPU:
                  32%          WindowServer
                   7%          com.apple.coremedia.videodecoder
                   4%          System Preferences
                   1%          EtreCheck
                   1%          Finder
    Top Processes by Memory:
              336 MB          Logos
              197 MB          mds_stores
              197 MB          WindowServer
              172 MB          Safari
              147 MB          com.apple.IconServicesAgent
    Virtual Memory Information:
              2.39 GB          Free RAM
              4.16 GB          Active RAM
              636 MB          Inactive RAM
              834 MB          Wired RAM
              2.08 GB          Page-ins
              0 B          Page-outs
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