I too use a HTPC for ALL my movie playback (bluray m2ts, 3d iso, mkv, avi, vob, etc) and don't have this issue. I play everything back through XBMC 12.0 Frodo which I highly recommend. In my XBMC settings, I have video playback set to "adjust display refresh rate to match video" and all my movies play back silky smooth.
With that said, MPC-HC, TMT5, PowerDVD, etc all play back my movies smoothly. I just prefer XBMC.