Why does autofocus keeps moving in and out on some slides

I can think of three possible reasons for the continuous focus adjustments: the autofocus system may have a bind; it might be in need of calibration; or the curvature of the slides keep changing because of the varying heat absorption rate of the transparency.
Unfortunately, aside from making sure that all the slides are in the same orientation as the tray, there isn't much that the average user can do to correct the continuous focus adjustments.

The lens focus ring is set and calibrated by the manufacturer using precision instruments like MTF testing benches and many other specialized tools, thus making it difficult for end users to perform any sort of manual adjustments. I would get in touch with the manufacturer to see if either repair or replacement would be a viable option.

The autofocus system isn't really "autofocus". It is a measuring system - you manually focus the first slide, which sets the distance from the front of the slide in the gate to the back of the projection lens. By the focus motor moving the projection lens, subsequent slides will maintain that same distance. Continuous focus adjustment suggests that:
1> The curvature of the slide is changing because of the varying heat absorption rate of the transparency.
2> The autofocus system is out of calibration.
3> The autofocus system has a bind (it is being restricted from free operation).
About the only thing a user can do is to make sure ALL slides are oriented the same way in the tray. Beyond that, you will need a service manual and 2 or 3 specialized tools. Parts and tools can be purchased from: www.micro-tools.com

Good Luck !! jim