In MP4s the chapters are encoded either as a text track with the chapter times/frame numbers and the text (QuictTime chapters). This text track is associated with at most one of the other tracks. Or as atoms (Nero chapter format)
Both HandBrake and MetaX support QT chapters only (for now).
HandBrake used to associate the chapters with the first audio track, however this was problematic when using multiple audio tracks (chapters would disappear when not listening to the first audio track), AAC/AC3 included, and also was a problem because HandBrake can encode with no audio at all.
MetaX assumes that the chapters are associated with this first audio track, and so everything worked smoothly.
HandBrake changed the chapter track to be associated with the video track instead, since that provided a more consistent approach, you are always watching the same video track.
MetaX has not been updated to change to use the first video track for the references. So although it reads the chapters OK, when it writes them back out it gets confused and doesn't write out the chapter text track at all, so the chapters are forever lost.
Rod (MetaX) has been informed of the issue on many occasions over many months, one can only assume that he's stopped maintaining MetaX and has moved on to other stuff.
In the meantime there are other tools becoming available for editing chapters, and you can always add them up front using HandBrake.
Cheers, Ed.