I updated handbrake-cli using aptitude upgrade, as well as the codecs and now when I try to convert a file it keeps giving me an error "MP4 muxer disabled". Does any one know what the problem is?
Yes. The repo version is broken. I found a comment from the author, I really can't remember where but he acknowledges the official version is no good.
Good news is that he's got a PPA that works well and works flawlessly on my system.
Here's the terminal stuff -
sudo apt-add-repository ppa:stebbins/handbrake-snapshots
sudo apt-get update
sudo apt-get upgrade
He said he'll get it fixed in due course, once he's figured out what went wrong.