Hmm, could you please list your filter chain, your PC specs and your SVP settings?
Failing that, I have a few suggestions that you could try:
On my G-Sync display, having G-Sync enabled caused a constant amount of frames being dropped, regardless of CPU/GPU usage.
Even if you don't have G-Sync, you could try changeing your display driver's profile settings for the mpc-hc.exe file, and setting the global default to use your custom settings. Specifically, you could try disableing all power-saving features (setting prefer maximum performance) and also try different ways of handling v-sync.
For v-sync, you should have the application (mpc-hc) handle it and not have any value forced in the display driver's control panel. You could also try manually adding dwm.exe (in C:\Windows\system32\) and forcing 'prefer maximum performance' as well as forcing v-sync 'off'. This could have an effect since I believe mpc-hc, by default, defers v-sync handling to the dwm.
I would also suggest that you use madVR as your renderrer, even if you do not use any of the advanced scaling features, simply because you can then very accurately specify the frame buffering and drawing behaviour, and you can also press CONTROL + J to bring up the performance statistics.
If these stats show that you are dropping small numbers of frames, even though your maximum frametimes over the 5 second window are well below the refresh frametime of your display, then it is almost certainly some sort of v-sync or other frame drawing / framerate matching problem and not one of purely insufficient performance.
Edit: Also, if you are using ReClock, be sure to specify the v-sync location at either the very top or the very bottom of the screen and to enable script notifications.