The new version of Handbrake, 0.9.3 writes chapter markers that are incompatible with the current version of MetaX. It will write the chapter markers but when MetaX tags the chapters you will lose the chapters all-together. I downgraded Handbrake back to 0.9.2 and all is working well again. I found the legacy version here:
http://www.brothersoft.com/handbrake-for-mac-68296.html
Hope this helps others to not have to re-encode multiple titles.
http://www.brothersoft.com/handbrake-for-mac-68296.html
Hope this helps others to not have to re-encode multiple titles.