Make sure you are connected to the USB_1 header on your motherboard. Had a report that connecting to USB_2 and leaving USB_1 empty caused issues.
I don't have a way to test Thunderbolt. My USB-C port works on the back though.
Also, try plugging directly into the motherboard, and not through a hub. I was having issues with devices disappearing after some time, and it stopped after I removed the USB 3.0 hub from the equation.
Try my EFI out. You should be able to use my exact EFI for that board and CPU. As far as I know, the only thing Designare EX has is the optional wifi card thing.
Also, reset your BIOS and load optimized defaults. If I recall, there are some settings in the BIOS that change how USB is handled by...
I had this issue when I was using the wrong FakeCPUID in config.plist. I use 0x0306a0 currently.
It may also be related to your OsxAptioFix2Drv. I use the free2000 version...