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I used Server 2012 with Hyper-V enabled on this very same machine, with no problem. Something changed in R2 because as soon as I enable it and reboot, my video card is no longer recognized, the 2nd display doesn't work and when I go to re-install the video drivers (nVidia Quadro 600), it can't find the card. I'm pretty sure that I called Microsoft or otherwise got definitive information from them that there was no fi…
Did you try manually installing the Quadro drivers? It sounds like it's not so much a Hyper-V issue as a 2012 R2 issue.