Both windows won't go all the way up
 

I have a 99 M3 coupe which sits a lot and the battery has gone dead in the past, but I have had a maintaner on it for a while. I have had the windows down about an inch to avoid mold/mildew buildup. Recently I started it up to move it out to the driveway and the windows won't roll up. I have tried holding down till the windows are down and 5 sec past to reset with the key in the "ON" position with no success. I have also done the key turn in the door lock to raise the window. I know that with the door open the alarm beeps 3 times with the remote when locking and unlocking, but not when the door is closed. (Meaning the open/close switches are working). Also, the door doesn't lock with the remote, but does when I use the key, then both doors lock/unlock. Maybe I am not doing one of these resets correctly or is there something else?

Have you tried running the windows all the way down then up and hold 5 sec.? That is the window initialization procedure. (Not down and hold for 5 sec.) Although the on-line service manual says if not initialized it will block the "tip" function (?) and the clamping protection is not activated. I don't know if that includes what you described in your issue.
For the locks, all I found is a diagram of the key positions (in the driver's door key cylinder I assume) where it shows a 100 degree turn clockwise to a position called synchronize. Not sure what that does. If you feel brave or lucky you might try putting it in that position then operate fob? I'm guessing myself so maybe that's not a good idea. Have you checked the owner's manual for programing a fob or tried holding lock and unlock for 3-5 sec. to see what happens first. Again, guessing. If you can't figure it out, my suggestion would be to try a locksmith, before the dealer, they may know how to re-program the fob and save you some bucks.