I suggest checking operation of all the switches in the system, Peter. When a switch closes to signal the controller, it does so by completing a circuit from the controller to chassis ground. All of the switches are wired to the "Y" connector of the soft top controller. You'll need a basic multimeter or other device for measuring continuity between the inputs and ground.

To access, open the storage compartment behind the passenger seat. Remove the plastic cover that protects the soft top controller by loosening three 10mm plastic nuts. The "Y" connector is the long black one (there are two others as well -- the "X" and "Z" connectors). Now remove the two 10mm nuts that are securing the controller and lift it off of its mounting studs. Now you should be able to easily separate the "X" connector from the controller.

Looking at the connector you will see two rows of sockets numbered sequentially. Nearly all of these are inputs from the switches, though some are not used. You proceed by putting the top in "Position 1" and checking all the switches and then repeating the same for "Position 2". The info below shows which inputs should be open and which should be closed for each position. Have the ignition off while you perform your checks. Note that you only need to check 17 inputs.

Position 1 (Top closed, windows up, roll bar up)
Open: 10, 22, 27, 29, 30, 31
Closed: 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28

Position 2 (Top open but storage compartment cover open, windows and roll bar down)
Open: 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 28
Closed: 10, 22, 27, 29, 30, 31