I guess go back to the beginning.
Step 1. Make a backup of wallet.dat
Step 2. Remove every file in the bitcoin folder except for wallet.dat
Step 3. Launch bitcoin and let it download all the blocks again.
--------
If that still doesn't give you a solution, then you might try pywallet to export the private keys and import them elsewhere.
I've done that (re-download block chain), but those transactions still show.
I can't seem to figure out how to export keys, or import them back (in bulk) into a new wallet using pywallet. Know of a tutorial anywhere?