I have the reinhold installed on my M and the windows still work fine,
you have to re-initialize the windows,
It actually tells you how to do it in the cars manual,
Or there is a load of threads on the internet,
From what I remember,
Turn key on but don't start the engine,
bring the windows down fully, Press down again 4 times within 10 seconds,
bring the windows up fully and keep holding the switch 2 seconds after they reach the top (don't let it go the whole time)
Then after 2 seconds bring the windows down about 4 inches,
Then bring them back up and hold for another 2 seconds,
Thats it,
Sounds like a PITA but I had to do the same thing last week as my drivers side stopped the "auto up" thing and I did the above process and its all gravy now