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If you take the wiper arm off of the pivot for the wiper motor and run the wipers until they stop and shut them off does the window work every time?
If the wiper is not returning to the home position the rear window will not work correctly. If you can get it to return to the home position then remove the negative battery cable and operate the power window switch for the rear window from the center console hold it to the Auto down position until the window goes all the way down then release it and immediately go to the auto up position and hold it till the window stops for about 3 seconds. This is the only way to retime the window while in the home position on the wiper if that still does not continue to allow the window to work you will probably have to replace the wiper motor.