"I went to the bank to get my $0.40 back out, and it wasn't even the same $0.40, I checked the mint marks on the dimes! The bank teller told me that they have a computerized balance that shows how many dollars I have, but clearly they are just taking someone else's money to pay me back mine!"
This. MtGox is a huge coin mixing service, no reason to break that functionality. You can still see your total deposits in the blockchain, but the balance won't be accurate.