I just returned an ASUS X99 Deluxe with similar issues. It would detect the Warthog joystick, throttle, and Saitek combat rudder pedals just fine no matter if I plugged them into USB 2.0 or 3.0. The issue was if I left any of them plugged into any USB port and rebooted, the computer would freeze right after POST during windows logo animation. After a few days I lost a couple of USB 3.0 ports altogether. It would also boot into basic BIOS randomly as well.
I currently have an ASROCK X99 Extreme4 Mobo. It has the same issues - if I leave the joystick, throttle or rudder pedals plugged in during a reboot or startup. Nothing else seems to cause this problem. Devices like Track IR, Wireless headset seem to work fine during boot, but not joysticks, throttles or pedals - weird. It maybe an X99 thing and UEFI Bios / USB thing.
I hope someone could shed some light on this.