The Spinning Wheel

Hello,
When I tried to sleep my computer last night as is my habit, I had the spinning wheel going on the desktop screen.  I finally gave up and went to bed only to wake up this morning with the wheel still spinning. In trying to troubleshoot I went to disc utility/first aid and clicked on verify disc permissions.  A couple of items jumped out at me...
User differs on "System/Library/Java/JavaVirtual Machines/ 1.6.0.jdk/Contents/Home/lib"  Should be 0 is 95
Warning SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified will not be repaired.
After running permissions repair I decided to start the process over again with "verify permissions" only to find that all the original permissions variances came up just as they were the first time.
What is going on with this?  Help.
Thanks

As long as the report ends up with 'Permissions repair complete' then, as far as permissions go, you are fine. You can ignore the various statements in the report:
Permissions you can ignore on 10.5 onwards:
http://support.apple.com/kb/TS1448
Using 'should be -rw-r--r-- , they are lrw-r--r--' as an example, you will see the that the permissions are not changed, but the | indicates a different location. This is because an update to Leopard onwards changed the location of a number of system components.
Poster rccharles has provided this description of what it all means:
drwxrwxrwx
d = directory
r = read
w = write
x = executeable program
drwxrwxrwx
|  |  |
|  |   all other users not in first two types
|  | 
|  group

owner
a little more info
Before the user had read & write. A member of the group had read.
After, only the user had read & write.

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    [loaded]com.avast.AvastFileShield (2.1.0 - SDK 10.9) Support
    [loaded]com.avast.PacketForwarder (1.4 - SDK 10.9) Support
    [not loaded]com.devguru.driver.CDFree (0.1.8) Support
    [not loaded]com.devguru.driver.DevGuruVsp (0.1.8) Support
    [loaded]com.logmein.driver.LogMeInSoundDriver (1.0.3 - SDK 10.5) Support
    [not loaded]com.parallels.kext.prl_usb_connect (7.0 15107.796624) Support
    [loaded]com.vmware.kext.vmci (3.1.4) Support
    [loaded]com.vmware.kext.vmioplug (3.1.4) Support
    [loaded]com.vmware.kext.vmnet (3.1.4) Support
    [loaded]com.vmware.kext.vmx86 (3.1.4) Support
    Startup Items:
    HP IO: Path: /Library/StartupItems/HP IO
    Launch Daemons:
    [loaded]com.adobe.fpsaud.plist Support
    [loaded]com.adobe.SwitchBoard.plist Support
    [loaded]com.ambrosiasw.ambrosiaaudiosupporthelper.daemon.plist Support
    [loaded]com.avast.init.plist Support
    [loaded]com.avast.uninstall.plist Support
    [loaded]com.avast.update.plist Support
    [loaded]com.cloudpath.maccmd.plist Support
    [running]com.crashplan.engine.plist Support
    [loaded]com.google.keystone.daemon.plist Support
    [not loaded]com.logmein.logmeinblanker.plist Support
    [running]com.logmein.logmeinserver.plist Support
    [loaded]com.logmein.raupdate.plist Support
    [loaded]com.oracle.java.Helper-Tool.plist Support
    [loaded]com.oracle.java.JavaUpdateHelper.plist Support
    [running]com.orbicule.uc.plist Support
    [running]com.parallels.desktop.launchdaemon.plist Support
    [loaded]com.vmware.launchd.vmware.plist Support
    Launch Agents:
    [not loaded]com.adobe.AAM.Updater-1.0.plist Support
    [loaded]com.avast.userinit.plist Support
    [loaded]com.google.keystone.agent.plist Support
    [loaded]com.hp.help.tocgenerator.plist Support
    [failed]com.logmein.LMILaunchAgentFixer.plist Support
    [running]com.logmein.logmeingui.plist Support
    [running]com.logmein.logmeinguiagent.plist Support
    [not loaded]com.logmein.logmeinguiagentatlogin.plist Support
    [loaded]com.oracle.java.Java-Updater.plist Support
    [running]com.orbicule.UCAgent.plist Support
    [loaded]com.parallels.desktop.launch.plist Support
    [loaded]com.parallels.DesktopControlAgent.plist Support
    [running]com.parallels.vm.prl_pcproxy.plist Support
    User Launch Agents:
    [loaded]com.adobe.ARM.[...].plist Support
    [loaded]com.adobe.ARM.[...].plist Support
    [running]com.akamai.single-user-client.plist Support
    [failed][email protected]
    [loaded]com.avast.home.userinit.plist Support
    User Login Items:
    CrashPlan menu bar
    VMware Fusion Start Menu
    Dropbox
    TeamViewer
    EvernoteHelper
    Internet Plug-ins:
    GlancePlugIn: Version: 2.5.6 - SDK 10.4 Support
    o1dbrowserplugin: Version: 5.4.2.18903 Support
    OfficeLiveBrowserPlugin: Version: 12.3.6 Support
    Flip4Mac WMV Plugin: Version: 3.2.0.16   - SDK 10.8 Support
    AdobePDFViewerNPAPI: Version: 10.1.10 Support
    FlashPlayer-10.6: Version: 14.0.0.145 - SDK 10.6 Support
    LogMeIn: Version: 1.0.935 - SDK 10.7 Support
    Silverlight: Version: 5.1.30317.0 - SDK 10.6 Support
    Flash Player: Version: 14.0.0.145 - SDK 10.6 Support
    iPhotoPhotocast: Version: 7.0
    CitrixICAClientPlugIn: Version: 11.1.0 Support
    googletalkbrowserplugin: Version: 5.4.2.18903 Support
    AdobePDFViewer: Version: 10.1.10 Support
    LogMeInSafari32: Version: 1.0.935 - SDK 10.7 Support
    QuickTime Plugin: Version: 7.7.1
    SharePointBrowserPlugin: Version: 14.1.2 Support
    JavaAppletPlugin: Version: Java 7 Update 60 Check version
    Safari Extensions:
    avast! Online Security: Version: 9.0.2022.120
    Audio Plug-ins:
    iSightAudio: Version: 7.7.1 - SDK 10.7
    iTunes Plug-ins:
    Quartz Composer Visualizer: Version: 1.3 - SDK 10.7
    User iTunes Plug-ins:
    TuneUp Visualizer: Version: 2.2.0 Support
    User Internet Plug-ins:
    CitrixOnlineWebDeploymentPlugin: Version: 1.0.26 Support
    WebEx64: Version: 1.0 Support
    3rd Party Preference Panes:
    Akamai NetSession Preferences  Support
    Citrix online plug-in  Support
    Flash Player  Support
    Flip4Mac WMV  Support
    Java  Support
    Perian  Support
    Time Machine:
    Time Machine not configured!
    Top Processes by CPU:
    6%WindowServer
    4%mdworker
    2%SystemUIServer
    0%LogMeIn
    0%configd
    Top Processes by Memory:
    113 MBCrashPlanService
    108 MBcom.avast.daemon
    108 MBDropbox
    92 MBFinder
    67 MBSystemUIServer
    Virtual Memory Information:
    2.61 GBFree RAM
    1.19 GBActive RAM
    651 MBInactive RAM
    573 MBWired RAM
    534 MBPage-ins
    0 BPage-outs
    There were two listed as [failed]:
    Launch Agents:
    [failed]com.logmein.LMILaunchAgentFixer.plist Support
    User Launch Agents:
    [failed][email protected]

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