Ok, Here is the deal. I don't think that it is the Microsoft update thing. The computer on which I am running the game is not connected to the internet. I would have no way of securing the update. However, I am pleased to say the problem is solved or at least successfully circumnavigated. There appears in the Starfleet Command main directory two .exe's that will run the game. One runs, that stupid "register now for prizes" thing, the intro movie, and the game, and one just runs the game. The programs menu shortcut is to the one that runs the junk and the game. This is also the one that I am having problems with. The other, though, the one that runs just the game, allows the hotkeys to work. So problem solved. Thanks for the replies and the helps. I don't know of any other game that the fans are so willing to help each other out even down to the technical support.
thanks,
Interstellar Machine