I don't know 100% but...
Have you looked in the BIOS to check the thunderbolt card is recognized - And activated - Thunderbolt requires 4 x PCI-e lanes I think
After this it could be an idea to get a thunderbolt driver from somewhere else, after all it is an Intel driver.
I had a strange experience with another motherboard by xyz manufacturer where rear USB 3 ports would not work which were controlled by a Renesas driver so I Googled Renesas as I'd never heard of them at that point. Anyway I used another Renesas driver somewhere else and it worked, not straight away but the USB ports started to work, weird really -
Check BIOS - Then source another driver if not working
Don't know what else to suggest apart from another PCI-e slot and maybe check there are no conflicts eg - If any other connections share the same bandwidth eg - SATA ports and or M.2 / U.2 slots if you have them - Post back to say how it goes - Thanks