I know this is not the case you are having but I did once have a weird error where the file count could not be resolved to the disk directory, resulting in a "Lost + Found" folder mysteriously appearing on the root level of the disk and every time I ran Disk Utility an entry to the folder was added. The SMS on the drive was incompatible with the SMS built into the computer resulting in an inconsistent count because the drive head would lock twice on movement. Maybe some kind of inconsistency in your case between the TM drive directory and the internal drive directory, a shot in the dark here.
