If both sides are moving, I might assume that would rule out motor or linkage problems but not totally sure on that.
But one thing that may cause the motors to get out of sycn is the way we do the extend/ retract part.
I had to fight my wife to get her to do it my way because she is trained to not work a motor once it stops! Good idea on a lot of things but this is designed to have us "overrun" past stop to allow the "heads/gears" on the tracks to sycn.
So something to consider and think about how you do things is if you do let the motor run for a few seconds past when the slide stops???
I may be blaming you for something you don't do but it might give you an easy fix?
The idea is that all motors will run slightly different and with different friction on each side, the slide with move different at different times, so they build the system with this in mind and recommend holding the button a bit after the slide stops moving!
Page 10-3 has info on where to find troubleshooting and referr to the manual that should have come in the big info case. Maybe good info on where to find the lights and what they mean?