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there is another thunderbolt port next to it that works fine
TB is strange, even if it's on the motherboard you may have mutiple hubs internally that are each coming alive in a specific sequence and that interaction with the motherboard (and then the OS) can be due to that sequence.
When I start my Windows system, on the BIOS screen it presents a "1 drive, 6 keyboards, 2 mice, 9 hubs" (or something to that extent)... and I know (because I once looked it up) that things like USB have a max number of ports per hub (and it's ~7) and that TB has a max bandwidth (and it's phenomenal)... and the result is that a lot of these things are logically daisy chained... I only have 1 real keyboard, and I do not have 9 hubs, I have a single TB hub, and the monitor has some extra ports... but this is evidence of the system design that is internally chaining.
With TB, one of those ports is the first hub... everything else is daisy chained off of the first.
My hunch... attach to the first hub if you can discover it and try and reproduce to see if this fixes it.
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Velocio
Thanks @se1derful and @Velocio
Desktop:
5950x / vision b550 d / vision 3090 / 64gb 3600 corsair vengeance rgb (2x32gb) / wd black sn850 4tb / noctua nh d15s / 4 x nf s12a / corsair 4000d airflow
The drive (sandisk 4tb extreme pro - not without their issues I know) is plugged in via an apple thunderbolt cable directly to the port on the motherboard. I never use it for other devices, just drives.
Thinking further on it, there is another thunderbolt port next to it that works fine...