I don't have the Service manuals manuals in front of me at the moment, but your description makes sense. I'll check later and report back if there's any additional news. Once the Folding Top Control Switch is enables, it would likely have a higher interrupt priority to the Folding Top Control module over the other switches. In instances where my rear deck lid would partially open, then close, (using local control switches) cycling the top often fixed the problem - for awhile.
A re-learn is the quickest way to determine of it's a dropped value or legitimate calibration/faulty sensor issue.
Another quick check for you Chip, would be visually inspecting and verifying the hydraulic fluid level above the hydraulic motor, then visually inspecting the rear deck lid hydraulic cylinders, hydraulic lines, and mechanical linkages.
From the symptoms you've described, it sure sounds a lot like a faulty sensor, but a dealer's scan and/or re-learn should quickly isolate the problem.
CCC