Other than MAYBE Miata's "reset" idea, I think Nick has the answer - water has leaked into the area where the TCM is and damaged it or corroded the connections.

But keep my comments in mind about a bad battery - if not for this problem, for future reference. Repeatedly, we have seen people pay hundreds of dollars in diagnostic fees only to find that a new battery fixes the car. And do not miss my point: The battery will "test" just fine, but will still fail in the car.

Also, I STILL don't think a bad limit switch explains this. I COULD be wrong, but to cause the top to go the 'wrong' way???? I'm not convinced either way.