When you release the latch to lower the top there is a micro-switch in there that signals the top controller that the latch is released. Yours might be stuck so the controller thinks the top is already up. Use your finger to wiggle the switch. This might be your problem. The windows work because they also think the top is up.
The little red clip fools the controller into thinking that the top is up so you can arm the alarm system with the top down.
Good luck.
derb
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