klrman :
Yeah, sorry about that. I had a difficult time understanding how handbrake works and then about using mp4box afterwards, but I understand it now. I read that handbrake should convert to mp4 in linux, but there is some debian bug which needs a workaround. I'm trying to wean myself completely off windows and will take your advice to heart and search much more before posting.
Yes, debian has issues with multimedia applications because of their use of 100% GNU/open source materials. You might want to start with a different distro if you are still learning and trying to use linux as main.
You'll find that learning how to search for what you need will help you elsewhere too, it's a great skill to have.