So I figured out the autorun & autoload of configs per mapped airplane. That is pretty slick btw. I mapped out a bunch of planes in both flight sims to configs and it works really well. Now, I also observed something weird. MobiFlight running and quit X-plane and start up MSFS2020, MobiFlight works fine and transitions well. However, when I quit MSFS2020 and then start up X-Plane 12, MobiFlight get stuck. It sees X-Plane running, but the plane it detects is showing one from MSFS2020. If I restart MobiFlight it immediately sees X-Plane, detects the correct aircraft, and auto-loads the correct config. So I think there is a glitch somewhere.
#Flipping between MSFS2020 & X-Plane 12 issue.
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Definitely looks like a bug. You can open an issue in GitHub, https://github.com/MobiFlight/MobiFlight-Connector/issues/new/choose
Thanks @pine fern - Will do.