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Doesn't fit the usual indexing issue. Could be simple but not likely. Could try disconnecting the battery for 10-30 minutes and see if that resets something, but again likely not going to help.
In most cases when a window doesn't go up or down all the way it is a regulator problem. I haven't dealt with it but apparently it isn't necessarily easy to see when in the door. The wires fray and get wrapped up in the mechanism and stops the progress in one direction.
If you look at this discussion and the ebay pic it might help you look for a problem with yours:
I have had the same problem. It is the wiring harness inside the door has come loose and is hanging under the window stopping it from rolling all the way down. Just remove the door panel find the harness and duct tap it to the door. Fixed.