I replaced the cylinders for my convertible top. I manually opened and closed the top twice to reset the control module and everything works, except one issue. When the tonneau cover closes it seems to latch, but the back window doesn't lower. I then opened it to look at the tonneau cover seating and the motor runs and it pulls the cover down, I here a latch noise, but it doesn't beep. When I release the switch, the motor stops and the cover pops up and is not latched. I adjusted the lock to every position posssible and it still acts the same way. I then disconnected the connector and the top acts the same way.
Question: would this be the limit switch in the lock? Why would the process continue with the connector disconnected? Am I running down the wrong rabbit hole?

Thanks in advance.