Let's think about this question, because I can't even begin to understand what must have happened.

We assume the MtGox kept an offline wallet with the bulk of Bitcoins in it. If anything else is true, the someone should simply string Karpeles up by the neck.

For 800k or so Bitcoins to vanish from an offline wallet scares me. I have my own (somewhat more modest) stash on Bitcoins in an offline wallet. If Gox can lose offline coins, has someone found a way to raid offline wallets? How? How?

Alternatively, if those Bitcoins were moved into the Gox hot wallet, we must assume that this took a fairly large number of moves. You would think that, for example, after 10k Bitcoins had been moved to the hot wallet a few times somebody would have asked some questions and started investigating. It is hard to see any scenario where 800k Bitcoins are moved from the Gox offline wallet to the hot wallet without Karpeles or someone else at Gox becoming aware that there was a serious Bitcoin leak.

So maybe the hint Karpeles gave in an IRC interview carries some truth. The Bitcoins are still there, but cannot be moved for some reason. For this to be true, the keys for that offline wallet must have become unavailable. Now, I have few Bitcoins compared to MtGox, but there are 3 backups of my offline wallet, one of which is stored in another country - we have to assume that an exchange would have better backups than an individual Bitcoin miner. Is it possible that Karpeles got careless with backups and something silly happened, like a USB stick became corrupt? It seems unlikely.

So... I cannot think of any sensible explanation for the apparent loss of appx. 800k Bitcoins.

In the absence of a credible explanation for the loss of the Bitcoins, my conclusion is that there is more to the story than we have been told, and Karpeles is being, if not downright dishonest, very economical with the truth. Can anybody think of any credible way for Gox to lose appx. 800k Bitcoins or to have had them stolen?

Can anything be learned from the blockchain? If enough people who have, at one time or another, moved Bitcoins to or from Gox were to publish transaction IDs maybe patterns would emerge - maybe we could find some of the Bitcoin addresses for the Gox offline wallet and see whether large numbers of Bitcoins have been moved out of it.