I would guess that maybe you have some problems with your 0.6+ wallet, and so exporting and re-importing the keys is probably the best thing to do anyway.
Then when I ran bitcoin-qt again, the transaction was no longer showing at all. It's still on blockchain.info as an unconfirmed transaction, and I'm sure it will eventually confirm, at which point I will see it in my wallet again.
My issue is that these transactions do not exist in the blockchain and were generated during a split. The transactions that
are showing on blockchain.info do not appear in my wallet... weird issue. I imagine that rebuilding a new wallet from the private keys should fix it though, since it re-verifies every transaction for every private key imported.