I recently had to re-do my HTPC due to a hardware failure. In doing so I decided to upgrade some things and start converting my uncompressed 30gb blu-ray rips down to m4v's, both to save space and for compatibility with iOS devices and extenders. I sware I had this working before the rebuild, but maybe not. Considering the severe lack of information on the internet on the subject, I assume I'm doing something wrong. My process has been to use MakeMKV to rip the main movie to MKV with only the chapters and TrueHD stream. So I'm taking those files and using handbrake to convert them to M4V's. I use the high profile setting with some tweaks depending on the movie (will increase quality to 18RF and leave the TrueHD bitstream in the file along with the new Dolby PLII stream for some movies). That's working all well and good. If I open the m4v file in VLC media player, the chapters are there and working. But no matter what I do I can't seem to get MPC-HC to recognize the chapters. I've followed numerous setup guides and keep coming up with nothing. I'd switch to VLC if it supported bit streaming, but alas, it does not.
The only thread I can find on the subject is this one: http://forum.doom9.org/showthread.php?t=164317 which talks about mpc-hc's inability to recognize "apple text" chapters. Having to de/re-mux all of my converts seems silly just for chapter markers that appear to be in tact. Plus I've already been converting these movies for a solid week and finally hit the half-way mark so I'd be pretty bummed to have to do further work on all of them. MPC-HC recognizes the chapters fine in the original MKV's, btw.
You can try to install my LAV Splitter to replace the MPC-HC builting source filter for MP4/M4V, while i am not sure i ever personally tested all kinds of mp4 chapters, reports from the thread you linked to seem to indicate that they work fine with LAV.
You can find numerous guides on how to use LAV here on the forum (look for "Advanced MPC-HC Setup Guide") or in other places on the web.
Yea I've tried the LAV filters and that guide. Tried preferring the LAV and blocking the haalli, and visa versa. I've also installed shark's codec pack which is what I've used for the past X number of years.
I got around a similar issue using MPC by splitting the main movie file at what would be chapter points, & then creating a custom playlist. It works best when there is an acceptable break in the video, as there would be between tv episodes, or some obvious cut scene. This way you can just jump ahead or back to each separate video file as if it were a chapter. It's a bit more work on the front end, but worth it to me for playback.