I tried the roof on the weekend and it worked as normal...fine from the fob and the buttons inside the car, and didn't work whilst driving the car.
I fit the Gaptech module on the weekend, and it works fine with this now.
@PKZ4 -Thank you very much for your offer, I really appreciate it. Seems like all is fine now though. I can only imagine that the roof module 'turned off' when the battery was low, and it took a while for it to come back to life (very technical explanation, I know!)