Permission repair will not repair

Folks....
A few weeks ago, I noticed that running permission repair from the HD I have booted from will not repair permissions. I have pages and pages of un repaired permissions. I booted to my Leopard DVD and ran permission repair from it and have the same issue.
I ran disk repair from the Leopard DVD and it said my HD was fine.
Suggestions? Maybe a 3rd party software package? Any shareware/freeware I might try first. I would hate to spend the money on Tech Tools Pro if it would not fix it. I started getting squirrely things happening, and freeze ups. But other then bad permissions, I can not find any thing wrong.
Thoughts? Thanks in advance.
jack

OK, Here is what I see when I try to do permission repairs. I am happy to hear you say some are not so bad. In the past, the OS fixed all of them. I was taught to run permission repair after each now software install. Maybe that is not correct?
Repairing permissions for “Jacks HD”
Reading permissions database.
Reading the permissions database can take several minutes.
Permissions differ on "System/Library/CoreServices/AirPort Base Station Agent.app/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "Applications/Utilities/AirPort Utility.app/Contents/CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/DVD.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSettings.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSources.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Movies.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Music.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Photos.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Podcasts.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/TV.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/BackRow.framework/Versions/A/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "Applications/iTunes.app/Contents/CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "Applications/iTunes.app/Contents/Frameworks/InternetUtilities.bundle/Contents/ CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "Applications/iTunes.app/Contents/Resources/iTunesHelper.app/Contents/CodeResou rces", should be -rw-rw-r-- , they are lrw-rw-r-- .
Warning: SUID file "System/Library/Filesystems/AppleShare/afpLoad" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/Resources /DiskManagementTool" has been modified and will not be repaired.
Warning: SUID file "sbin/umount" has been modified and will not be repaired.
Warning: SUID file "bin/rcp" has been modified and will not be repaired.
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Warning: SUID file "usr/bin/quota" has been modified and will not be repaired.
Warning: SUID file "usr/bin/rlogin" has been modified and will not be repaired.
Warning: SUID file "usr/bin/rsh" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DesktopServicesPriv.framework/Versions/A/Reso urces/Locum" has been modified and will not be repaired.
Warning: SUID file "System/Library/Extensions/webdavfs.kext/Contents/Resources/loadwebdav" has been modified and will not be repaired.
Warning: SUID file "usr/sbin/pppd" has been modified and will not be repaired.
Warning: SUID file "usr/sbin/vpnd" has been modified and will not be repaired.

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    Permissions differ on “System/Library/PreferencePanes/Displays.prefPane/Contents/Resources/Japanese.l proj/DisplaysPref.nib”; should be drwxr-xr-x ; they are -rw-r--r-- .
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