So Ukyo, is this it or what?
Bad WeExchange code related to transaction malleability caused the coins to be lost to people by repeated withdrawals?
This seems like quite possible explanation - some people mutated some transactions and then claimed their coins again and again until there were almost no coins in the weexchange wallet. They could be doing it quite some time and just keeping enough bitcoins in the wallet for daily withdraws (meanwhile monitoring the wallet by knowing some of the wallet public addresses - for example their own deposit addresses). In one point of time Ukyo started the manual transactions and shortly after he realized what happened. Just a speculation.