http://arxiv.org/abs/1403.6676I'm not in the 'karpeles is a theif' camp, I don't think anyone can actually know, and everyone who is damn sure they do know needs to check themselves.
However, this is the kind of evidence that makes it more of a possibility.
Malleability can cause huge accounting problems for an exchange that does not properly protect against it. Mt. Gox just found 200,000 Bitcoins in an unused wallet. This gels perfectly with the idea that has been circulating on Silk Road for a few days, where they allegedly posted the private information of the person who stole all of Silk Road 2's coins (Link
http://www.deepdotweb.com/2014/02/18/alleged-silk-road-2-0-hacker-doxxed/ ). Basically the person did steal some coins from Gox, but was really only trying to create huge negative media downfall to sell his coins at the earlier high price and buy back in at a low price. The attacker that was named had also done work on the Silk Road, and was an insider there, which explains how he hit them when they had all their coins in their hot wallet.
Karpeles is not an idiot, he knows he couldn't get away with stealing the coins, and if he tried he'd never be able to spend them or he would be killed. If you want to find informed information on this look at the posts regarding Silk Road. The developers there are more knowledgeable than almost anyone on Bitcoin and cryptography in general because if they aren't they serve hard time. These two stories are very linked, but the claim that only 400 coins were stolen gels perfectly with the fact that transaction malleability can only be used to steal coins in a hot wallet at an exchange, and that Gox had been earlier verified to have been holding all the coins and had claimed it had up to 98% of its coins in cold storage.
Transaction malleability doesn't actually change where coins are sent, it just makes them look like they went places they didn't meaning it makes perfect sense that Mt. Gox is saying they are finding coins in wallets they didn't know had any. Why would Karpeles steal coins that he could never use when he had an immensely profitable job as the head of an exchange? I'd be very surprised if Gox doesn't return at least 90% of user coins, and fully expect them to return 100%.