Up and down or in and out ? i'm getting ready to take mine out for a paint job. Did they ever fit right ? There is only so many adjustments to make, is everything installed properly ?
If you don't have to take those glasses and/or regulators out... DONT !
Now for the thread starter... What car ? Are these all OEM glasses ?
If you bought a used glass it may be wrong.
From my experience... you can spend enough time to get that window lined up with the door glass, come back later and renew the door hinges, the go back in to realign the quarter glass.