Well, this is a new one!

1) Does it do it if you drop the top and then put the windows up? If so, it is nothing to do with the top.
2) If only ONE window does it, I'd say you have a window mechanism problem.
3) If BOTH windows do it and ONLY when the top is up, keep reading.....

There is a switch in the frame around the windshield on the passenger side - the right hook from the top locking mechanism presses on the switch when the top is up - as you go to drop the top, when you turn the handle, the hook moves, letting the switch close - this signals the BCM to lower the windows. It sounds to me that this hook or the switch is loose, indicating to the BCM, for just a second, that you are lowing the top. So, for that second, it lowers the windows, then when the arm moves to press on the switch, the BCM stops commanding the windows to lower.

So....
Unlatch the top and verify that the right hook is not loose or insecure in any way. You can reach in there and see if the switch itself has come loose from it's mounting screws as well, - but I must say, in six years with there Crossfire Roadsters - I've never heard of this one.