Sounds like the motor is going out. You "program" the motor itself for the auto up/down feature and as the track and motor wears out the original calibration doesn't really work anymore. You can try to recalibrate it yourself which is fairly simple, remove the door panel, there is a little circle "window" that you reach into and push a rubber button on the motor itself while you roll the window back up manually "without using the auto-up function". I did this a couple times on mine before the motor failed completely and needed to be replaced so it's more of a band-aid fix but it will probably work.
This thread has good pictures to remove the door panel, takes about 30 seconds once you know how.
If you scroll down to the photos of the inner door panel you see a few "black textured looking round stickers" in various places on the metal inner panel, behind one of them at the bottom is the recalibration button. See post #12 by EPiK who has taken excellent pictures of exactly where it's located.
The reset procedure itself is lined out here, very simple, just pay attention to not using the auto up/down functions. You may have to do the recalibration multiple times to get it to finally work and that button needs to be depressed HARD, you will not feel a tactile "click".