Absolutely reeks of what I went through.
Initially (when I first was installing the card) I had to tear it down several times (remove driver, remove card. Boot. Shutdown. Add card, Add Drivers,....Repeat). Took two days.
For about a week I went through what you are going through until I arrived at my power down sequence. It has been 9 months now and my machines sees the Thunderbolt card on every boot unless I blow my power down sequence.
I just thought of something, 'Fast Boot' is really problematic with the Thunderbolt buss. I do not use fast boot. (See USB below).
I am not sure what a Windows 10 update could have possible changed other than the
boot order of your kernel mode drivers. I would be running a boot log. When I got a boot log that worked I would save it. When I get a boot that fails I would compare the two boot logs.
It is possible I suppose that the Windows 10 update has configured your machine to keep power applied to the USB ports when shut down
I am assuming that you have not touched the BIOS (plenty of relevant Thunderbolt setting there). If you have I would double check the BIOS settings.
USB:
I am not sure what brand/model your Thunderbolt card is. All Thunderbolt cards I am aware of are based on USB-C. So you PC will see parts of your Thunderbolt Interface on the USB Buss. Are your USB ports staying powered after you shut down? Do not believe any of the setting you have in Win10, plug something into the USB ports to see if they are powered after shut down. If so your Thunderbolt card is probably
staying powered.
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