Thank you SO MUCH for looking into this!! From the sounds of your comments, I was afraid you had decided this wasn't worth developing into a software fix.
No, I have never had issues with autofocus. When I do autofocus, I always get plenty of good stars. That being said, its possible that I'm avoiding the problem by using the option to "crop autofocus frames" by X percent. I used it for a long time when I wasn't using a field flattener, because I wanted to avoid using elongated stars for computing the HFR. My settings are currently to crop by 10%, but I'm not sure if that is enough to crop out the overscan regions. Can't take a sub right now to check, but I will net chance I get if you think it will help?