The flat battery might have caused a shorted circuitry in
your power window control unit, specifically the one you've
mentioned in question. The instrument cluster in my VW
van went haywire permanently when I tried to start the van
with an unknowingly almost totally flat battery 2 years
back. Had to replace the whole cluster itself. Not sure how, but it
just happens. It's best to have your car sent back to AD to have it
checked out if you want to rectify it.
btw, what car are you driving?