Might be XP leaving PnP devices in a state that either the BIOS or XP itself doesn't expect/doesn't deal with well on boot; That'll only show up on a warm-boot (bringing the ~RESET pin low is only going to reset the CPU and enter the BIOS)

Check to see if the BIOS has a setting as to if the OS is PnP aware. It's a bit of a long shot. :-)