I have been having the same problem with my windows. I took it to one dealership which replaced my driver's window motor but as you can suspect this did nothing to help with the problem. I then went to a different dealership and they have seemed to fix the problem.
The dealership reprogrammed my car to the 46.1 level programming. So far so good with the windows although I seem to have two new problems. For one, I can no longer open my top with my key fob. It randomly worked once but I can't get it to work again.
Also, now my "MyBMW" remote app no longer works.
Does anyone have a E93 at 46.1 with top functions working via the key fob? I think something was just programmed wrong, or at least I hope. It would be total BS if BMW just removed this feature as the SA is telling me.