I had drive problems after upgrading to Mountain Lion; however mine were more related to my external drive with iTunes randomly unmounting itself. Additionally my Superdrive kept spitting out DVDs and my console was a twitter with crash reports. My end solution was to wipe the internal drive, reinstall ML, and then manually re-installing applications.
During this process I had access to a fantasticly incredible Apple Senior Advisor. (not being sarcastic, we were like a dream team of user and tech. LOL) He had me mount the sparse.bundle image on my Time Machine backup (which is a Lacie NetworkMax 4TB drive) and then I could manually browse the backup via Finder. The dates of each incremental backup show up as folders. Under that folder, I then can see each drive that was backed up. That is how he had me manually get my /User files back.
Additionally, I asked about when I feel like my current and refreshed setup was stable how Time Machine would react. He said it would either start a new or conclude the machine is the same and just do an incremental backup. If it starts a new backup, I will most likely need to clear some space eventually. In order to do that, he said to mount the sparse.bundle (double click or right click/mount). You can then right click and delete the backup.backup (or whatever its called). That will clear your space for your new Time Machine backup.
Sorry that if this is overly verbose. I just wanted to make sure I stated the original problem, how it was resolved, and then expalin the options I was told to use to clean up prior backups.
I hope that helps!