Skuzzy,
When the game launches I'm assuming one of the house keeping chores it does is to tell the OS to suspend screen saver mode\power saving mode.
Is there any chance if the USB power management option: "Let the computer turn off this device to save power."
is checked in the power management tab for USB Root HUBs in Device Manager that an occasional errant USB device reset is possible if the flight controler is not touched for the time out period set for the screen saver?
I have Saitek X52 Pro and Pro Peddals.
Thanks, Skuzzy....