Sounds like a driver issue to me.
Some graphics card drivers do filter the video output by default, other drivers do not. On my XP system I'm using the ForceWare drivers 71.89 for an old GeForce and the video output is bilinear filtered by default. On my Vista system I'm using the ForceWare drivers 188.22 and the video output is not bilinear filtered by default, not even if I activate the bilinear filtering.
Do you get a filtered video output, if you use the "nearest neighbor" filter? On both of my systems, I get a clear unfiltered output with this filter.
Unfortunately I have no solution for your performance problem. As long as I have no high-performance filter like "NTSC" in use, the frame rate almost never drops below 60.