Well, I started examining the USB and boot settings, and before I did much in the way of experiments, I noticed that my mouse worked on boot (I have a boot manager that boots first and can take mouse input), but not the keyboard. So I moved the keyboard USB plug to a different port on the motherboard, and amazingly... it started working, even while the USB3 hub was plugged in.
I'm guessing it has something to do with which path each USB3 port takes; some I guess are connected to the internal USB3 hub on the motherboard, others connected directly to the chipset USB3 support; I am guessing that perhaps the ports attached to the internal hub aren't fully activated at boot time, or perhaps they are and it's the Intel ports that have conflicts.
I can't say I know why, but merely swapping ports on the back enabled the keyboard at boot time.
Very very weird.
- Tim