My "guess" is that the opener and door on the way down are causing the screw gear to get bent such that the engagement isn't straight anymore.
One thing I've noticed that seems to not only make garage door openers last longer but also tend to take up alot of the bouncing and wear and tear is to mount the opener with plumber's tape so it's "suspended" and can actually get some flex in it. I have an ancient door opener (at least 25 years old) mounted to a box frame in the rafters via plumbers tape and it still works like a champ and takes up all the flex.