Maybe check your mappings for any control that might be bound to a pause command.
As there are two pause commands, for each type, one to set and another to unset, if you inadvertently activate pause, it might cause the issue you are experiencing. Just do a search for “pause” in your assignments for each controller.
I had previously had to clear the pause mappings that I had deliberately allocated to the pinky switch of my warthog throttle, which is quite easy to inadvertently flick, as I had experienced some similar odd behaviour during flights and this was a potential cause. Although I can’t be certain that this had caused my issue, I haven’t seen it since.