I use Handbrake as well, so I thought I would share a couple of settings pages. The attached are from a DVD conversion of Crouching Tiger, Hidden Dragon (I also upscaled it to 1080p and it looks very good!). In the Audio page, I use the passthrough option mentioned above, there were originally two other tracks that were both in stereo only, so I deleted those. In the Video page, I use the H.264 QSV encoder option with the Same as Source framerate which automatically changes it to the variable framerate setting. Also, I find changing the Constant Quality to 20 works fine for me.