I hope everyone's issues have been resolved since this thread started, it's been awhile. I've just dealt with the same issue on an Gigabyte X99-UD4 motherboard, and I'm also using thunderbolt for an audio interface. My motherboard died, showed no signs of life. Turns out the BIOS chip failed, so it was repaired under warranty by Gigabyte. Unfortunately the BIOS version I was using at the time was either F12 or F13b, and when it came back it had been updated to F22. My system wouldn't recognize the GC-Thunderbolt 2 add-in card in either slots PCIE_2 or 3, nothing else had changed and the software was still properly installed.
I was successfully able to downgrade the BIOS to F20 since I can't go past that version, and now it works fine. Perhaps when the motherboard re-detects peripherals after a BIOS update, it provides the option to enable and disable?