I'm having difficulties with my top, too...here is what happens:

When I unlatch the front, the windows don't go down, and the light on the switch blinks. If I lower the top manually, make sure it locks, etc., I can raise it automatically. When it gets to the end of the travel, and is ready to latch again, I get the same beeps from the switch that I did when I tried to lower it. Do I understand correctly that the windows are supposed to go down when you unlatch the top, and if not, the front sensor on the passenger side is bad?