Ah, got it. This is definitely a BIOS related issue.
Legacy USB Support - Try setting this to Disable and retest. If that doesn't work, see if moving the wheel and keyboard to different ports helps. If you are using a hub, remove it and connect directly to the boards ports. Not a whole lot you can do in this situation if the ports remain powered after shutdown. BIOS downgrade is another possible solution since you stated an earlier rev worked previously.