Best I can tell, the windows anti-pinch safety feature is controlled by sensing the current draw of the motor. Which will change as the motor wears, and thus will need to be re-calibrated from time to time.
And the way your windows are reacting, it does sound like the control module is erronously sensing that the window encountered an obstacle before fully closing, thus reversing itself so as NOT to pinch someone's arm in the window.
The above procedure, in simplier terms. Close the window the whole way, pull up on the window switch the whole way and hold it at least a full second. You'll hear/feel the motor push the window against the stops for at least a full second after you release the switch. This will give the module a new value for the current drawn when the motor is powered but stopped (stalled). The windows auto up and down feature should work fine for a while.
If your motor is really wearing (or gumming up inside, which is how most window motors go bad) it will require this re-calibration more and more often.
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