You can safely ignore certain messages that Disk Utility reports when checking permissions. For example, you may safely ignore a message that contains "permissions are 33261". This article applies to Mac OS X 10.2.2 or later.
You can safely ignore any message that begins with "We are using special permissions for..." or "We are using a special uid for...". These are status messages and not a cause for concern. The message(s) will appear each time you check permissions.
After running periodic monthly messages such as this may appear and can also be safely ignored: "Permissions differ on ./private/var/log/install.log, should be -rw-r--r-- , they are -rw-r----- Owner and group corrected on ./private/var/log/install.log Permissions corrected on ./private/var/log/install.log"