My card also stops working after a while. Since I use my home PC every weekend and remains unpowered during weekdays, TBEX3 vanishes from BIOS completely. It's not detected in the NB Agent as a x4 adapter at all. All I have to do to remedy this is to take these steps:
i. Reset to BIOS defaults with the button at the back,
ii. Enter my settings manually or by loading from stored profile,
iii. TURN OFF Thunderbolt (in Advanced Menu),
iv. Save and boot in Windows (remember, no TB at this stage, it's off in the BIOS),
v. Restart and once inside BIOS, turn ON Thunderbolt and careful to set the correct NB or SB and Pciex slot,
vi. Save and boot in Windows, TB functional again,
vii. Repeat procedure every weekend.
Hope this helps
Same problem here with the card suddenly disappearing from Windows 😮 Right now it shows as USB 3.1 controller. But the ThunderBolt part has vanished. God only knows why.
Asus, can you please do something ? 🙂