Still missing those coins. It really is quite perplexing. The dates of the transactions with those coins are all from the june/july 2013 range and up until 0.9.1 were valid confirmed coins, and are now conflicted transactions and missing coins. Does this mean I was passed bad transactions previously and it's only now showing up? If so, how were those coins spendable prior?
Do one thing, import wallet on blockchain.info then make a new wallet and send coins to your qt wallet. (Make sure to send a test amount first)