I've tried that before without luck (logged in normally and booted from the install disk), just tried it again now and I've had no luck again. Looking at what it does change it doesn't seem to touch the AirPortBaseStationAgent...
One thing I have noticed is that if I re-run the repair permissions it will literally repair the same permissions again. It's like it's not saving it when it's done....
Repairing permissions for “Macintosh HD”
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_TW.lproj/RemoteDesktopMenu.nib" , should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_TW.lproj/RemoteDesktopMenu.nib" .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_TW.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_TW.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_TW.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_TW.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/zh_TW.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/zh_TW.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_CN.lproj/RemoteDesktopMenu.nib" , should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/zh_CN.lproj/RemoteDesktopMenu.nib" .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_CN.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/zh_CN.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_CN.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/zh_CN.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/zh_CN.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/zh_CN.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/ko.lproj/RemoteDesktopMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/ko.lproj/RemoteDesktopMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/ko.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/ko.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/ko.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/ko.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/ko.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/ko.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Dutch.lproj/RemoteDesktopMenu.nib" , should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Dutch.lproj/RemoteDesktopMenu.nib" .
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Dutch.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Dutch.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Dutch.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Dutch.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Dutch.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Dutch.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Italian.lproj/RemoteDesktopMenu.ni b", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Italian.lproj/RemoteDesktopMenu.ni b".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Italian.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Italian.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Italian.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Italian.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Italian.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Italian.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Spanish.lproj/RemoteDesktopMenu.ni b", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Spanish.lproj/RemoteDesktopMenu.ni b".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Spanish.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Spanish.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Spanish.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Spanish.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Spanish.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Spanish.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/French.lproj/RemoteDesktopMenu.nib ", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/French.lproj/RemoteDesktopMenu.nib ".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/French.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/French.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/French.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/French.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/French.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/French.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/German.lproj/RemoteDesktopMenu.nib ", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/German.lproj/RemoteDesktopMenu.nib ".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/German.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/German.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/German.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/German.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/German.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/German.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Japanese.lproj/RemoteDesktopMenu.n ib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/Japanese.lproj/RemoteDesktopMenu.n ib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Japanese.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/Japanese.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Japanese.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/Japanese.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Japanese.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/Japanese.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/English.lproj/RemoteDesktopMenu.ni b", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/Menu Extras/RemoteDesktop.menu/Contents/Resources/English.lproj/RemoteDesktopMenu.ni b".
Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent" has been modified and will not be repaired.
Permissions differ on "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/English.lproj/UIAgent.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/Support/Rem ote Desktop Message.app/Contents/Resources/English.lproj/UIAgent.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/English.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreen.app/Contents/Resources/English.lproj/MainMenu.nib".
Permissions differ on "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/English.lproj/MainMenu.nib", should be drwxr-xr-x , they are -rwxr-xr-x .
Repaired "System/Library/CoreServices/RemoteManagement/AppleVNCServer.bundle/Contents/Su pport/LockScreenLeopard386.app/Contents/Resources/English.lproj/MainMenu.nib".
Permissions differ on "Library/Application Support/Apple/ParentalControls", should be drwxrwxr-x , they are drwxr-xr-x .
Repaired "Library/Application Support/Apple/ParentalControls".
Permissions differ on "Library/Application Support/Apple/ParentalControls/ALRHelperJobs", should be drwxrwxr-x , they are drwxr-xr-x .
Repaired "Library/Application Support/Apple/ParentalControls/ALRHelperJobs".
Permissions repair complete