"Or, MtGox themselves see that they’ve been watching for transaction for too long and could automatically re-send another transaction" There is no amount of ti

"Or, MtGox themselves see that they’ve been watching for transaction for too long and could automatically re-send another transaction" There is no amount of time to wait until a bitcoin transaction is considered dead. Once its been communicated over the network, one has to assume it can be redeemed (incorporated into the blockchain) anywhere from never to a thousand years from now. Checking for txid even without malleable transactions is not helpful. If a bitcoin payment has been issued, and a customer wishes it to be re-issued, the (only?) safe approach is to move the entire address contents to a new address, wait for that to hit the blockchain, and reissue the payment from the new address. When different customer's balances are mixed in the same address, things get more difficult, and seeing as how its customary to pull balances from multiple addresses to satisfy the inputs a single transaction, I think mtgox has a claim to complexity beyond their ability to fix without help from the protocol itself. As far as being affected by malleable transactions, an exchange should have a value on their 'books' for each customer and a value in the 'bank'/wallet for each customer. By keeping track of each set of addresses for each customer, like bitcoind does in its wallet, the two can be audited with each new block on the chain.