The rain rail is easily damaged when installing, but I do not know how it would get damaged on an original top. It is not such a big deal to take off the carpet (do not pull on the carpet to get off the plastic "nails"; use a fork or equivalent) and unscrew the nuts holding the brackets. Then gently pry open the rain rail and check for garbage or damage. Damage can be fixed with electricians tape.
Other ideas: (1) Check the rubber weather strips around the window. Their position is adjustable, but mark the original position first before unscrewing anything. (2) You might have tiny holes in the side of the top. The reason is the top material getting pinched at the point where the top frame hits its stop. There are updated brackets that avoid this. See TSB at finishline.com (Or is that finishlineperformance.com?)
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