FYI, BB
Below is a quote from Apple describing what Disk Permissions deals with.
If you still need assistance, please describe what problem/issue you are trying to solve.
http://support.apple.com/kb/HT1452
"Many things you install in Mac OS X are installed from package files (whose filename extension is ".pkg"). Each time something is installed from a package file, a "Bill of Materials" file (whose filename extension is ".bom") is stored in the package's receipt file, which is kept in /Library/Receipts/ in Mac OS X v10.5 and earlier. These files don't take up much disk space and you shouldn't put them in the Trash. Each of those ".bom" files contains a list of the files installed by that package, and the proper permissions for each file.
Does Disk Utility check permissions on all files?
Files that aren't installed as part of an Apple-originated installer package are not listed in a receipt and therefore are not checked. For example, if you install an application using a non-Apple installer application, or by copying it from a disk image, network volume, or other disk instead of installing it via Installer, a receipt file isn't created."
Is this what you want to "fix"?