Software used: X-plane 11.05r1 and Linux Mint 17.2, both fully updated.
Hardware used:
1. A Saitek Yoke System consisting of a Saitek Pro Flight Yoke and a 3-lever quadrant module.
2. Saitek Pro Flight Rudder Pedals.
3. Fast PC Tower
X-Plane tells me that "the device 'Saitek Saitek Pro Flight Yoke' needs to be calibrated". Notice that 'Saitek' is mentioned twice by the software. On the top left of the calibration page only one device is available, namely the "Saitek Saitek Pro Flight Yoke" (twice Saitek again). No mention of the 3-lever quadrant module nor of the Rudder pedals. All above hardware works just fine in Flightgear, another simulator, so the problem must be in the X-plane 11 software. The Yoke and quadrant module can be manually calibrated and saved as the default configuration, but upon a restart, this hardware is again not recognised by X-plane 11 and the previously saved default configuration cannot be reset. The rudder pedals can't be calibrated.