I just made a full backup with Time Machine. Ran it yesterday, and then again today. I have two hard drives installed in my Mac. The primary drive has the OS, Applications, data, etc. The secondary drive has some additional files.
Previously I was running Mountain Lion on a Case Sensitive, Journaled file system (primary drive). I erased the drive and made it a Case Insensitive, Journaled file system. After reinstalling Mountain Lion and trying to restore from Time Machine it only saw my secondary hard drive (which didn't get erased, so was pointless to restore from). I skipped the Timemachine restore at that point, and figured I would try the Migration assistant.
Once Mountain Lion booted I opened Time Machine and could see the backups for both drives. They both appeared to be intact. So I tried Migration Assistant, and it also only reported seeing the secondary hard drive and unable to restore any apps or user data.
How do I troubleshoot this? I went back into time machine, and it appears to have everything there, so I could restore individual files, but I would really like to restore everything - applications, settings, documents, etc. I've used Timemachine a few times to restore after a full erase and never had this much trouble.
Update: I patched the new install of Mountain Lion to the latest updates, in case that was the issue. Didn't help. I rebooted into OS X Recovery and selected "Restore From Time Machine Backup". It sees the external drive where the Time Machine backups live, but reports "No OS X system backups were found."