It honestly sounds like the two transmissions are just out of sync a bit; you can unhook the cable from one, and briefly press the button to move the top, get them aligned (use a tape measure to verify they are at the same location; Wayne's book has a good write up on how to adjust the clamshell / top transmissions.
1) unhook the cable from one side of the convertible top motor, and turn it with a drill (or just use the top button to turn the still connected one)
2) repeat until they are the same height:
Oh, and Buy Wayne's book!
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