PErmissions repair says done, but second repair shows same issues

After I repair permissions, a list of repaired files is shown and "Permissions repair complete". I decided to run it again immediately just on a lark. The same list of files appeared and the same "Permissions repair complete". I booted to the Leopard install DVD and ran permissions repair -- twice -- same issue. I know an Archive install will fix it, but any other suggestions? Use Pacifist to extract and replace the troubled files?

Repairing permissions for “Mac OS”
Reading permissions database.
Reading the permissions database can take several minutes.
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 "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/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-- .
Permissions differ on "Library/Internet Plug-Ins/JavaPluginCocoa.bundle/Contents/CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "System/Library/CoreServices/Archive Utility.app/Contents/Resources/Archives.prefPane/Contents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AVRCPAgent.app/Contents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Advanced.plugin/Co ntents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/AppleTalk.plugin/C ontents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Bluetooth.plugin/C ontents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Fax.plugin/Content s/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/IP.plugin/Contents /CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/SMB.plugin/Content s/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Uber.plugin/Conten ts/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Uber.plugin/Conten ts/PlugIns/Uber-AppleTalk.plugin/Contents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Uber.plugin/Conten ts/PlugIns/Uber-CUPS.plugin/Contents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Uber.plugin/Conten ts/PlugIns/Uber-Netinfo.plugin/Contents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions differ on "System/Library/CoreServices/AddPrinter.app/Contents/PlugIns/Uber.plugin/Conten ts/PlugIns/Uber-USB.plugin/Contents/CodeResources", should be lrwxr-xr-x , they are -rwxr-xr-x .
Permissions repair complete

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PErmissions repair says done, but second repair shows same issues

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