I just call a call from the Thor service department and we may have fixed the problem over the phone! It seems that if you stop running the slide motors in the middle of the stroke the motor revolutions in the coast down phase are not counted and the front and rear get out of time with each other. All I had to do was run the slide in and out a couple of times without letting off the button until it stopped. I don't believe that the dealer told me that during the checkout. I have been letting it stop part way out to check outside clearances before going all of the way. They also sent me a PDF on how to shim the racks on the Lippert drive motors. They want me to take it to dealer to have it done for warrentee reasons but at least I can check it now. They are also going to send me the shims so that when I go to the dealer I won't have to wait for parts and hopefully will get it done the same day.
I am going to go shop for one of those chucks with the straight end on it.
Thanks.