Hm.
Only thing I can suggest is to take the motor off, manually push the window all the way up, and then put the motor back on. This would at least be a place to start to see if the problem is with the motor. If you can't push the window all the way up, then the problem is with the window itself. Check to see if the back edge is properly mounted - if it's 1/2" off, there's your problem.