I had a similiar issue, my car is in storage for four months during the winter, when I bring it back out for use I could get the top 99% down and it would stop indicating the partition wasn't down. I would end up putting the top back up and check the micro switches. That was my issue, the switches would not send the signal that the top was all the way down. Dealer replaced two switched under warranty but when I got the car home, same issue. I ended up spraying silicon on the switches.
2005 ML 350 Black on Black, K&N, 20's, Privacy Tint, Bose 114K and runs strong.
2006 CLK 350 Iridium Silver, convertible, K&N, 32K cream puff. Wife's toy...