What is a D9400? Google isn't helping me...
Most likely the reflash hasn't worked right. Have you got taken the pristine bios and modded that again and tried it?
So, on your older (Win 8.0? Win 7) setup, you had an Atom-15 flashed card, and crt_emudriver installed, and you could see the post screens during boot and then windows came up fine and your games worked as desired, yes? And you haven't changed any hardware or done anything else apart from upgrade to Win 8.1, which you did while this machine was in the configuration above?
I would scruple to guess that your doing the latter has led windows to make some odd choices. A clean copy of windows would be advised, although i think it being a bios problem is more likely.