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. This is expected. Some applications are designed to be installed in one of those ways.
Also, certain files whose permissions can be changed during normal usage without affecting their function are intentionally not checked.