I use "subler" on Mac OS to mux my mp4's, and the resulting files' chapters play perfectly in MPC-HC. You can also insert those cool chapter thumbnails with it (that iTunes and iPads/iPods display), but beware that neither Haali or MadVR will play these files correctly, as they see the two video streams (actually one video one jpeg) and get confused.
Try using the latest build of MPC-HC, maybe that will work:
http://www.xvidvideo.ru/media-player...inema-x86-x64/