The left window lowered switch or its associated wiring may be bad. This switch is located in the bottom middle area of the door.

The lowering of the window is controlled by a single output from the soft top controller. The controller will turn this on if it receives an input to lower from the manual control switch. And during a lowering sequence the controller turns the output on until it receives an input from the window lowered switch.

Since your manual control switch functions, the output from the controller must be okay. And since the entire lowering sequence is initiated from a single input from the power top switch, this switch too must be okay. So, one is lead to deduce that the contoller is falsely receiving an input that the window is lowered when it actually is not. If so, this would be caused by the switch being faulty or a short circuit in the wiring between the switch and the controller.

Someone else may have a more plausible explanation for your problem. If not and you are interesting in testing the window lowered switch, indicate so and I will post a follow-up.

And hey. Any time you are having a problem with the soft top control system it is uselful to check for the presence of diagnostic codes as explained in this thread: http://www.peachparts.com/shopforum/showthread.php?threadid=38215