'Doc, your problem is surely one of the switches that detect the locked/unlocked state of each lock for the leading edge of the top at the windshield. The rear hatch (compartment cover) does not close until the controller is signalled that both sides are locked. It is possible for the top to appear locked but not quite tightly enough for both switches to close. I once had a car where the weatherstripping seal on the top had come loose at one place, and this was enough to cause the problem described.

Also -- I'm not sure, but I think the switches are adjustable. If so, maybe you need to remove the cover over the windshield to access the switches and adjust them to effectively lower the threshold at which they close.