MP4tools first processes individual tracks and then muxes them together to create an MP4 (or M4V) video. If there is no MP4 video when done, then some error occurred somewhere in the process. Among the temporary files created by MP4tools are ".log" files for each of the various processes that were completed. Look in those for a hint at the error. If you were passing thru DTS audio for example, MP4tools would extract it, but DTS audio can't be muxed into an MP4 file, so no MP4 video would be created. The first place to start would be the muxing log file.
BTW, you can turn of the creation of these temporary files in the preferences. It can get a bit messy.