The window guides are adjustable. Loosen the top bolt on the end of the door and try the switch again; the window should self-guide to its preferred spot. Re-tighten. If this doesn't improve things, the central connection from the glass to the lifting bracket may need shimming in or out. Again, loosen things and see if this is an improvement. Finally, the fabric inside the channels rots, balls up and increases the drag on the glass as its moving. You may need to replace the inner fabric. Pantera vendors all carry this stuff, fairly cheap.
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