Okay, so having discussed this already on the Handbrake forums, it seems the latest builds of Handbrake write both QuickTime-format chapters and Nero-format chapters to the output MP4 file. Unfortunately, when mp3Tag encounters an MP4 file with the Nero-style chapters, it becomes impossible to tag. Attempting to edit the tags results in all changes being reverted and all the chapter titles being changed to whatever was entered into the Title field.
Bumping this thread (I know there are many other like it based on a search).
As of version 15 of XBMC/Kodi (Isengard alpha 2), Video chapters are supported:
It would be great if the issue described in this thread and others (such as /t/14808/1 ) around mp4 chapters resulting in mp3tag not being able to tag gets resolved.
rebumping as it's still an issue (but thank you cause I found it via a search too.
Deleting Nero style chapters but leaving Quicktime ones intact allows mp3Tag to work properly. I used mp4tags from mp4v2 to do so (and to add chapters too):
(file won't work with mp3tags, tags won't save)
mp4chaps -r -N file.mp4
(file now works with mp3tags, tags save)