I dont know where the relay would be in your car but logic would suggest the same place. My windows were both working well during this fault. The mechanic said the connector into the relay was shorting, draining my battery like yours. (The largest of the 3 plugs going into the relay.)
Disconnecting this plug stopped my windows working but fixed the battery fault while I was waiting for the replacement relay. You could try disconnecting these plugs and see if it is the problem? :)
Having now fitted a replacement relay I have noticed the battery returning to full strength, a problem with my radiator fan not running has disappeared and the passenger window goes all the way down with one touch of the switch!
I have no idea if these were connected but as long as it remains that way, I wont loose any sleep.