Gox was robbed of a massive amount of coins (800k+) at some prior point in time, possibly June 2011, and has been operating a fractional reserve since.

Gox determined that it was better to continue operating the exchange, probably both for the sake of Bitcoin, and for their customers who would eventually be made whole from fees earned.

Gox knew of transaction malleability and had been keeping that scapegoat in their back pocket to use in the event of a bank run.  Or, they didn't know but the losses from TM were actually recent and minor.  Or, they didn't know but the losses from TM occurred over a long period of time and they never noticed because they never reconciled the books, because they knew they wouldn't match anyway because they were already fractional.