I wish I had some help to offer. That definitely sounds annoying. The only advice I can think of is that if it is at all possible to mess with that kind of stuff it would definitely be BIOS related. That's where I'd start looking. Then I guess look for some way to edit the order of powered devices and see if reordering helps at all. Sorry I don't have an answer. As for drive speeds I'm sure you could google that with acceptable results.
check to see if there any bios updates for usb fixes. I would also see if there are any usb drivers updates. i would also check to see if your bios has any usb handoff. sounds like it a usb handoff issue between the mb bios and windows boot.