I had the same problem. It's definitely because the program isn't recognizing the controller. Are you running Vista? Look in the very bottom left corner of the controller window, it looks like you'll have to drag the window up a little to even see it. You should either see "status: ok" or "no unit found." If you watch that corner when you first open up the program it scrolls through a couple other things too. But, I couldn't do anything to get it to recognize the multicontroller on my Vista computer. I had to run XP to get it to recognize the controller.
On the Vista computer I already had the .NET framework installed, I don't know if that could cause issues somehow. Other than that, the only difference I noticed is that it kept bringing up the standard install peripheral window on the vista computer, but it never did that on the XP computer. I just ignored it when it popped up on the vista computer.
Try an XP computer for now if you can, other than that, I don't want to make any suggestions. I'd hate to be responsible for damaging it somehow.