The hacking of the Gawker network a few days ago resulted in the leaking of user account information - including email addresses and passwords.

One (potentially more) of those email/password combinations was used by a Fur Affinity administrator. Someone (be they furry or not) noticed this and used the information to access the persons Fur Affinity account - getting administrative powers in the process. They used this time to fuck shit up.

FA was promptly taken offline (within half an hour, I heard) to prevent things going on and to investigate what had happened.

The more recent downtime has been because someone found an exploit in the code, or so I've heard. I'm not sure.