I'm no expert on the mechanics of the convertible top. Actually, shame on me, I've owned this car 6 years now and never really took the time to familiarize myself with how the roof operates.
But... I have had several experiences with it not working. The flashing yellow light always happened when the storage compartment wasn't properly folded down. I did get a solid red one time. It happened when I tried to operate the top with the car in motion (it was starting to rain and I pushed the button to close it before coming to a complete stop.) Obviously there is a motion sensor that can stop the top from working. Maybe that could be the issue? If so, it would be cheaper to replace (I would think) than some of the other possibilities.
Just a thought.. good luck, and let us know what ultimately happens.