It's also possible to exclude items from backups to from system>preferences>Time Machine. I have a whopping X-Plane installation (75GB) which i don't allow TM to backup. I have a backup copy on my R4, so there is no need to take up all that space on my TC.
Download TimeTrackar from http://www.charlessoft.com and you can use it to see the total size of each backup, which files were backed up backups and their size.
You may know this, but certain types of files, databases are prime examples, can quickly fill a Time Machine hard drive up very quickly. This is because you can make a very small change to a record, however the system will insist on backing up the entire file again.
For this reason it is recommended that you back up these files differently and exclude them from TM.
I appreciate this might not be the cause of your problem, but figured I'd throw it out there as no one else had yet.