I had the X-55 and it spontaneous fired commands now and then, even without VR. It turned out, that it did not receive enough power. This might explain, why your X-56 works without VR, but not with the HMD online.
Maybe plugging joystick and controller into different usb-controllers might help. Usually, the front and rear usb ports on a case are on separate usb controllers.
Otherwise, you might use a powered usb hub for the joystick and throttle. I can't tell, if this will help, but this was definitely a known issue.