I had a similar problem with my 97 E36 Coupe. Here are a few things I tried.
1. roll window all the way down and hold the button for about 5-10 seconds. Someone told me that resets the window motor, then push up and it should go up
2. manually (with the key) unlocked and locked and unlocked (held the key in the unlock position for about 5-10 seconds) the door from the outside. after this it the windows whent right up
Not sure what did it, but those are the two things I tried in my coupe.
Current Rides: 964 C2
Past Rides: 94 318is, 97 M3, 01 C2 Cab, 02 330ci, 06 323i, 05 330cic M Sport, 02 M3