The same thing happened to me, and it turned out to be the lever connecting the gear mechanism to the window. It had developed a crack, which gradually widened, so the window would not raise all the way, and it gradually got worse until the lever actually broke. I was able to get it welded, and it works fine again now. You might want to check yours -- if that's the problem, welding might be easier before it actually breaks. I don't advise replacing the entire mechanism -- I think it costs in the neighborhood of $500, even with a discount.
Chris