You said that "If I use the controller to override the system, it goes in and out as smooth as silk." That would tend to eliminate the slide out of square or the jacks causing binding. I suggest that you calibrate the slide:
1. With slide in.
2. Press Slide Extend button three times very fast to get in program mode.
3. Immediately press Slide Retract button and hold until motor stops making sound.
4. Repeat steps 2 and 3 five times.
You can reverse these procedures If the slide is out.
It is not well covered but ALWAYS HOLD THE BUTTON IN FOR AT LEAST 5 SECONDS AFTER THE SLIDE STOPS MOVING. EITHER RETRACTING OR EXTENDING. This will keep the motors calibrated. Make every effort to not stop part way when either opening or closing.