The windows operate in conjunction with the soft top controller. There are a pair of relays on the controller, one for each window. There are a pair of fuses in the trunk, one for each window. The usual culprit for what you describe is the actual window switch in the console, but not always. If the windows goes up and down when you operate the soft top, then the relays and fuses are OK. Do a SL forum search on windows and soft top controller, as there is a lot of information on this subject posted.

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