I am thinking you might have to recalibrate the windows....
Taken from manual:
Short drop glass (Front windows only)
In order to improve door efforts and sealing, your vehicle is equipped
with short drop glass. This feature lowers the glass when either door is
opened. The glass returns to its closed position when the door is closed.
Proper operation of the short drop glass requires that the windows be
calibrated. Though your windows will have been calibrated before
your vehicle is delivered to you, it is possible for the windows to
lose calibration. If a window loses its calibration, your short drop
feature will lower the window, but will not raise it again when the door is
closed. To re-calibrate the window, pull the switch up to raise the
window until it completes its travel and hold the switch up for 2
seconds. Another possible effect of lost calibration is that the feature
may not lower the window. To re-calibrate the window in this case, lower
the window until it completes its travel and hold the switch down for 2
seconds. Immediately after releasing the window down switch, pull the
switch up to raise the window until it completes its travel and hold the
switch up for 2 seconds. Perform Short drop re-calibration with
doors closed only. Re-Calibrating with doors open will cause the
window to continuously bounce back.
Rear Power Windows (Convertible Only)
The rear quarter windows are operated by a single window switch
located at the Driver door window controls. Press and pull the window
switch to open and close the windows.
• Push down and hold the switch to open.
• Pull up and hold the switch to close.
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