This has been resolved, and you are encouraged to register for the Fall Term. Welcome back! You will be registering as a graduate student, since you are coming back for the final year of your MENG program.
Uhm, er, I wasn't going back for the master's, really, but whatever it takes to untangle the bureaucracy there. And if I happen to satisfy the bachelor's degree requirements and then decide I've had enough, they shouldn't be able to do anything about it except... d'oh... put up more red tape and hurdles.
I'm not going into a lot of detail right now, but suffice it to say that MIT has more independent units of bureaucracy than I remembered, and they all did a bit of finger-pointing and buck-passing before I found someone at the top who wasn't on vacation.
But anyway, I'm still going to think about going for spring term instead of fall because of the scheduling conflicts / lack of writing class this term. Now to cajole an unsuspecting professor into being my advisor through this mess, and looking into getting the late reg. fee waived due to circumstances.