@5631klaus Sorry you're dealing with this issue. The problem you're describing matches some symptoms that I'm very familiar with, but I haven't seen anyone mention them in a while.
This happens as a result of the hot-swapping GPS units fighting for control over the autopilot, but usually happens after changing the avionics selection. Again, I haven't heard of it happening for anyone in a while, however. It's also happened that something in the community folder is conflicting, like some modification for a GPS unit. Have you tried this with a completely empty community folder and no hardware connected? In theory, that would be the best test. I think you might be right that the frame rate issue could be related, but possibly causal. If there is a huge delay between the avionics loading and the aircraft configuring itself, it's possible that might cause the issue. Perhaps if you find the source of your frame rate issues, the problem might solve itself.
Sorry that's not a definitive answer, but I hope it gives you some direction. You might also have some luck writing to Just Flight Support. They've helped many of my users with GPS/Autopilot related issues, and might have some troubleshooting tricks up their sleeves. In the meantime, I'm happy to help here!