From what I read, someone would send a coin and then change the transaction ID so it looked as though it didn't go through.  They'd contact Gox, and Gox would look and not find the transaction ID in the blockchain.  So they would send new coins.  Meanwhile, the coin they thought they didn't spend (But really did) went to the bottom of the coin pile.  

If we assume that whoever was doing this was moving large numbers of coins, it's possible Gox ran out of good coins.

Certainly they have some coins left that are good though.  Probably they cashed those out when they realized the majority of their money is gone.

I agree he probably had Cold Storage, but was his cold storage filled with bogus coins?  

Sounds like we could all speculate on this but until anyone performs a full investigation we won't ever know the truth.