So it sounds like the obstacle detection needs fixing. You don't happen to have those in-channel vent visors, do you?
I've posted the below before and you must follow it 100%, especially #7.
Window Motor Initialization
NOTE:Initialization is required to learn both the full up and full down positions and the profile of the glass as it travels through the glass channel. Once initialized, obstacle detection is enabled. This procedure is only required for Navigator (LF and RF) or Expedition (LF only) window motors.
NOTE: The window motor must be reinitialized whenever: the motor is removed from window regulator drum housing, a new motoris installed, a new window regulator is installed, new window glass is installed, glass top run removal or installation is carried out or when carrying out any operation in which grease or lubricants are applied to the window system. All window components (window glass, window regulator, window motor and glass top run) must be installed and tightened to specification before carrying out this procedure. Refer to the De-Initialization Procedure prior to performing the window motor initialization (unless a new motor is being installed).
NOTE: A new (or de-initialized) LF/RF (Navigator) or LF (Expedition) window motor will not operate in one-touch up or one-touch down mode until initialized. If a new LF/RF window motor has been installed, proceed to the Window Motor Initialization procedure in this section.
NOTE: Excessive bounce-back (window reverses direction with no obstructions present) may indicate that a de-initialization procedure may need to be performed.
De-Initialization Procedure
1.Start with the ignition key in the RUN position and open one front door.
2.NOTE: Steps 2 and 3 must be performed within 8 seconds.
Turn the ignition key from OFF to RUN 5 times.
3.Press the window control switch to the one-touch DOWN position (second detent) and release.
Window Motor Initialization
WARNING: Keep objects and body parts clear of the glass panel when carrying out the initialization procedure. During the initialization procedure, the glass panel closes with high force and cannot detect objects in its path. Failure to follow this instruction may result in serious personal injury.
4.Start with the ignition key in the OFF position and with the LF/RF door open.
5.Turn the ignition key to the ON position.
6.Activate and hold the window control switch in the one-touch DOWN position (second detent) until the window glass stalls for 2 seconds at the bottom of its travel and release the switch.
7.NOTE: After performing this step, wait a minimum of 3 seconds before operating the window control switch or ignition switch.
Activate and hold the window control switch (with no interuptions) in the one-touch UP position (second detent) until the window glass stalls for 2 seconds into the glass top run and release the switch.
8.Verify correct operation of the window by carrying out the one-touch up and one-touch down features. If the window does not operate correctly, carefully repeat this procedure.
