My guess is there is something stuck or a problem in the latch.

 

I would do a manual open/close and see if it clears the error. First though, do a hard reset at the battery (disconnect negative terminal and briefly touch positive), see if the battery drain was a cause.

 

you might find better help in the XK forum since we don't have drop tops on XJ8s.

 

didn't see it was in the XJ section! nice catch ross

 

Your roof is operated by hydraulics and a series if relays and switches and the icing on the cake is that it is all controlled be your security and body control module. When the battery went down your system went out of sequence. Charge your battery, check your latch locked properly with the allen wrench and give it a try again. From what you are saying the latch is open and you need to close it first before the windows will close. The windows open first and close last after everything is the way it is supposed to be. Removing the power and reconnecting is at times necessary but when you remove the cable remove it and when you connect it back trying doing it without creating static and count to ten before going back.