My setup is a little different than yours, however, not by much.
My printer, mouse, and scanner are plugged into a USB hub. The scanner and printer activate when I power up the computer [during POST].
My ancient motherboard BIOS does not permit me to use a mouse [while in BIOS], so, at present I do not need a mouse at that time.
I am tempted to build a new computer, however, this ancient Gigabyte P35-DS3R motherboard is still chugging away with a QX9650 CPU and AMD HD 6950 plugged into it and does everything I need it to.
Too bad I am not ready do spend money yet, I love to get the maximum stable yet long lived overclock. May be if I talked myself into 3 high resolution screens
It sounds as though you have tried every option available to you regarding your issue. I am aware that several motherboards that have the same USB problem. In your case I would hate to spend hundreds of dollars upgrading when all you have is currently a minor inconvenience.
If I need to boot into something other than Windows I make a bootable disk. Personally, I have not found the need for a bootable USB drive.