I don't have enough knowledge, but could it be that this "Money Services Business (MSB) Accounts, Identification of an MSB Customer" filled by Gox 2011 lost his legitimation or correctness after the recent FinCEN guidelines? I'm not even sure, if they define BTC as currency. Would love to hear some more details, if relevant.
It sounds like a lawyer fail on MtGox's part. The DHS knows about CampBX, they do the same thing (also through Dwolla). If this is all because they didn't properly setup/register the LLC, it's even less of a big deal then anyone could have expected. They'll probably pay a fine and pay some lawyers to set things up properly. Clearly the DHS isn't after Bitcoin or trying to shut down MtGox. The company MtGox setup in the USA was poorly planned/executed and got them in hot water. I'd imagine this gets resolved within a few months.