2005 beetle top is constantly confused...under warranty but VW is stumped too?

Our 2005 beetle had a top problem last week where it wouldn't go back up. The top wouldn't pull down and secure completely to complete the cycle. VW replaced some sensors and it will now go down but sometimes we have to roll windows up, down, up and sit for like 5 mins to get the top to seat down where the motor clicks to keep the alarm from chiming. Then it's fine. I've done all the obvious and it's driving us nuts. Summary: The top won't complete the "down" cycle and won't let it go back up until it does. Any ideas ?