I'm having this same problem as well, on my Lenovo Yoga 2 Pro under Windows 8.1. My native resolution is 3200x1800 (which is what I run, with 200% font sizing), so without scaling I get a ridiculously small centered window for my games. It seems that I've always had this problem on every DirectX 10 and 11 game (but not DirectX 9).
I've updated to the latest driver (.3960), I'm using DirectX 11, and I've tested with just one game recently (Bioshock Infinite, but other games have failed in the past too). Still having the problem. When I look in my Intel Graphics Options under "Panel Fit", the only option I have is "Maintain Display Scaling".