If I open controls settings in-game, my HOTAS disappears from the list of devices and stops being visible ingame until game is restarted
Forums topic: http://forums.bistudio.com/showthread.php?191380-X-55-stops-working-after-opening-controls
Video: http://www.youtube.com/watch?v=GkNCxD6HXII&t=5m30s
Devices known to be affected so far:
Saitek X-55 Rhino
MS Sidewinder Force Feedback 2
Logitech 3D Pro
I doubt it is related to specific device - seems more like a game bug to me - but, nevertheless.