Also try to shut down ATX features:
Fiddle around with BIOS and try to disable soft-pwr-off button and anything else that makes shutting down the computer to be windows compatible: if it fixes anything - problem is in software.
Fiddle around with BIOS and try to disable soft-pwr-off button and anything else that makes shutting down the computer to be windows compatible: if it fixes anything - problem is in software.