I'm glad to find this thread - but it seems that Asus pays no attention to it...
I have the same symptoms others have described here. See the attached mobo pic where I have numbered the PCIe slots for clarity. My slot #1 is occupied with a GPU card, as is usual, so it is not part of the discussion here.
I have two PCIe multi-port USB3 adapter cards that I need to use. These are known good since I just took them out of a much older Asus ROG Formula mobo where they worked fine. From their specs it seems that they require only PCIe x1.
--> My problem is that I can use only one of these USB3 adapter cards, and only if I install it in slot #4. Neither of these adapters will work in slots #2,3,5, or 6.
Asus really needs to address this. How is it there are so few complaints? I'm on BIOS ver 1201.
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Oh - but the silly colored lights seem fine. Every time I open the case to move the USB cards around, there they are, blinking away...