Yeah, it is weird. But there has to be something in either your setup or your procedure or we would all have the issue. So the issue is clearly something we would never expect!
One super stab in the dark, but, are your USB ports set to power down if a stick isn’t used? That is Windows’s default behaviour. I turn off power savings to all my devices, but I’m sure most don’t so like I say. I know it causes funny stuff in other games but not heard anything concerning MSFS.