If it were so cut and dry they wouldn't have chased his signature years later before the acquisition. A lawyer told them to do that.
I think it's more interesting of a legal case than you give it credit for. He isn't denying he was paid for his time but that the rights for the finished work are still ambiguous.
If the chance of a legal case going against Microsoft is 0.1% (e.g. his case is really bad), the estimated damages in such a case are enormous (I have no idea what they would be, but e.g. a tiny payment for every copy of Minecraft would be an enormous sum), and the cost of sending him an email is a couple of hundred dollars worth of legal counsel, then why wouldn't they chase him for a signature?
