This talks about the issue:
http://software.intel.com/en-us/articles/video-frame-display-synchronization
I have a feeling that with Reclock you do NOT want to force vsync. I may be wrong but I think I get the occasional "bad vsync" issues you describe, fixed by a fresh seek, when vsync is forced. They may well be caused by what is described in Fig 5. It's what we talked about some time ago with Haali. Things go wrong when you are very close, but not quite close enough to the right refresh rate. Unless you are very unlucky at the start, all is fine for a while, and then you hit the point where all hell breaks loose, as in Fig 5.
You remember that "little wobble" in the MPC-HC jitter you always hated when selecting VMR9 D3D. It may well be that this is exactly the kind of "best fit refresh cycle for each frame " described, i.e a positive feature designed to avoid the problems illustrated when slightly imperfect clocks synchronise in the wrong part of the refresh cycle as in Fig 5.