Mine (in the first Red Roadster) got all confused and refused to move one time. ON a theory, I did this:

Start car.
Put top down manually.
Put top up manually.
Shut car off.

Start car again - now it works fine.

My theory:
The TCM got all confused about where the cylinders were, that is, where in the cycle things were when it depressurized. By going thru all of this WITH THE ENGINE/KEY ON, the TCM got a chance to synchronize.

Or, maybe, as George said, the time it took for me to do all of this was enough for it to come back to it's brains.

If you don't know how to put the top up and down manually, you sure as hell better learn - before you get caught in the rain with a dead battery or a top that wont move for some odd reason. See my most popular video for instructions: