Disk utility won't repair permissions (related to error -8003)

I have an odd, recurring problem I can't diagnose. Recently my seven-month-old MacBook Pro has begun showing an error code (-8003) when I try to do common, system-related things like empty the Trash. At the same time, Time Machine stops backing up and Disk Utility can't repair permissions. If I go into System Preferences I can't open the lock to make changes, even though my account is still clearly marked as the Admin account. All third-party applications run fine, so I can't quite figure out what's going on.
I've tried repairing the disk via TechTool to see if there was directory damage and it checks out fine. I've reformatted my TM backup disk with Disk Utiity according to Apple's instructions, used the Terminal to ensure my Trash and old TM files were properly deleted, etc. Nothing seems to have made a difference.
When I restart the problem goes away for a couple of hours and then – at some point that I haven't been able to identify – the problem starts up again. This is the case whether I'm working on the MacBook or if it's just sitting there idle.
Before I reinstall I wondered if anyone had run into a similar problem and had figured out what caused it.

error code (-8003) when I try to do common, system-related things like empty the Trash
That's a common symptom of throwing stuff from a Time Machine backup into the trash in the Finder, which is a big no-no and can irreversibly corrupt your backup.  In the Terminal, type the following command:
sudo rm -rf ~/.Trash/*
Copy and paste that!  Don't try to re-type it, I've seen people put a space in the wrong place and wipe their whole user folder.  Type your password when prompted, and expect that nothing will show until you hit return.
Next, repair your Time Machine backup according to:
http://web.me.com/pondini/Time_Machine/A5.html
At the same time, Time Machine stops backing up
If the above troubleshooting doesn't fix your backup, you may have damaged it beyond repair.  In that case, you'll have to erase it and start your backups over from scratch.
Disk Utility can't repair permissions
Where are you trying to repair permissions?  Note that repairing permissions is only meaningful on a drive with a system installed on it, and only repairs permissions on a specific subset of the stuff on the drive.  Also, note that there are permissions messages you can safely ignore...  if you think it is failing because you're seeing them over and over, it's not failing.
If I go into System Preferences I can't open the lock to make changes, even though my account is still clearly marked as the Admin account.
I've never seen that before, and it may indicate you have much more serious problems with your computer.  First, try repairing your hard drive with Disk Utility.  Then trash the System Preferences preference file, located at:
~/Library/Preferences/com.apple.systempreferences.plist
...where '~' means "your home folder".

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    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/pt_PT.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/pt_PT.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/pt_PT.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/pt.lproj/UIAgent.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/pt.lproj/UIAgent.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/pt.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/pt.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/pt.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/pt.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/sv.lproj/UIAgent.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/sv.lproj/UIAgent.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/sv.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/sv.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/sv.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/sv.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/ru.lproj/UIAgent.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/ru.lproj/UIAgent.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/ru.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/ru.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/ru.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/ru.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/no.lproj/UIAgent.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/no.lproj/UIAgent.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/no.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/no.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/no.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/no.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/fi.lproj/UIAgent.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/fi.lproj/UIAgent.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/fi.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/fi.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/fi.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/fi.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/da.lproj/UIAgent.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/da.lproj/UIAgent.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/da.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/da.lproj/MainMenu.nib”
    Permissions differ on “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/da.lproj/MainMenu.nib”; should be -rw-r--r-- ; they are drw-r--r-- .
    Repaired  “System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/da.lproj/MainMenu.nib”
    Permissions repair complete

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