Autopilot shouldn’t affect it. At least it did not with Patagonia, but just to be sure I did fly it without in the Balkans and it did not work. I had no trouble with anything, the whole thing went perfectly.
Flying around, even landing at wrong airports and restarting shouldn’t hurt either. I did that a lot on Nevada as the plane didn’t have an AP and I was very new to the game. It worked perfectly the first time (Patagonia took me 2, but I used AP both times). However in one spot it cut a corner rather far from the point. I think that caused it to fail the 1st time as that’s the only change between my two flights.
I think there may be some small thing that triggers or fails it and we just don’t know what that is. You got lucky, most of us don’t lol
It definitely needs a fix. Or at least a specification that tells us what we need to do or shoudn’t do.