Does the transaction show up on blockchain.info? If so, it actually succeeded. Blockchain.info won't show it unless it's a valid transaction. It might just be taking forever to be mined...? Maybe it's showing it as empty because you just moved the coins out of it with a valid transaction?
If you aren't talking about blockchain.info, and the coins haven't moved and it appears to be trying to spend coins that don't exist, then it sounds like the database state is out of whack. You can use Help->Rescan Databases. If that doesn't work, try Help-Rebuild & Rescan.
A rebuild is a last resort, taking a couple hours, but should resolve all issues related to the DB.