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I would checking you switch works and is sending a signal ,second headliner doesn't need to come out, the console on the roof where crawl control and most likely your sunroof switch is should some straight off there you will have access to switch and the only plug to the sunroof motor
If there was a short it would be more intermittent , instead of choosing when and when not to work , i would look into the towns manual for the initialization procedure for the sunroof , sounds more like a miss communication happaning , example I can give is how sometime unplugging an window switch on some cars the auto up down function just stops working , but unplugging the battery it doesn't, and some cars unplugging the battery just confuses the entire car .
