Yes, however they have claimed that several hundred thousand bitcoin was lost due to malleability, and this would have happened over several years
That's what never clicked with me. Even you are a stoner monkey running a business, you would still notice cold wallet balance decreasing by several hundred thousand coins, especially over several years. Even dumb php sites can add "money in minus money out" to check where they stand at. So Mark definitely knew that he owed way more than he had. 100% certain.
If I recall correctly Karpeles/Gox claimed that they lost the coins recently due to malleability.
Anything else would have implied that they were conducting gross mismanagement as the missing coins would have had to show in their bookkeeping.
I don't know if there exists a log of all broadcast transactions rather than just those that are in the blockchain.
If anyone has such a log it might be possible to determine if and how many transactions were affected by malleability.
I am almost certain it was not the reason that the coins are "gone".
One very strong indicator that something fishy is going on is that the public information provided by Gox does not properly add up.
You cannot lose that amount of coinage over a long time with proper procedures without noticing.
Over a shorter period we would see other tell-tale signs like a noticeable change in bitcoin days destroyed.
The sheer amount of coins makes them very hard to hide if they were indeed stolen. It is easy to conceal a few dollar bills you stole but try to hide truckloads of money without it being noticed.
