Sorry to revive an old thread but having the same issue and hoping someone was able to figure it out. In my case, when opening, tonneau cover gets stuck at halfway lifted until I press the button again once or twice. When going back up tonneau lifts without issue. I am thinking it’s a micro switch or something for safety since it only happens when going down.

 

Not 100%, but it sounds like your issue is due to the tonneau deck lid motors that are located inside the trunk. There is one on each side. They are very similar the to the motors used to operate the windows and use brushes that get worn down over time with use. If I were you, I would start there.