I don't think anybody yet knows.

Note that it could also be negligence and fraud. For example, they might have discovered the losses early but hushed them up in hopes of making it up later. That's a classic way massive financial issues happen.

However, the transparency of Bitcoin only helps if it's used that way. There have been proposals to develop approaches so that anybody can externally verify an exchange or "bank". But as far as I know, MtGox hasn't released enough information for other people to verify their story.