Based on the available evidence, it appears that Gox lost a fairly modest amount of money (in terms of USD) in 2011 that compromises a decent bulk of the missing money. They were subsequently hacked a number of times that have been publicly reported, during which they likely lost some amount of money.

I am not entirely sure why the losses compounded over time, maybe Gox was not a profitable operation, and they took customer money to fund the losses.

Security did not seem to be a strength of Gox's. If they had been honest about the loss in 2011, it would likely have been not a very big deal, but Gox would have closed and some other exchange would have taken the spot of having the majority of trading volume.