BadWolfRacing
First thing in the morning, I will explore.
Menu bar-Tools
-Options
-Output files
The last selection is "MP4 file extension"
pulldown menu has "Automatic" "Always use M4V" "Always use MP4"
I would stay with .mp4 and away from the Automatic for your purposes as you have already found.
https://trac.handbrake.fr/wiki/Containers
http://forums.macrumors.com/showthread.php?t=441377
Thanks for the follow ups.
ATR