The system thinks you did not complete the last cycle. And, it sounds like you didn't. This can be the switch you refer to, or the bow switch or the latch switch in the frame of the windshield.
Also, if the top is not working because of water damage to the CLP/SSM, that could also confuse the system and would mean you must replace the CLP/SSM and last few feet of the wiring harness leading to the CLP/SSM as well.