I had the same problem. I created the file using Handbrake and ran the resulting mp4 and it worked in iTunes. I tagged the file with MetaX and lost the audio track. I did this twice with the same results. Previous versions of MetaX did not do this. This is the update. I will send a bug report.
Don't use the toggle like you did on previous versions, because it also now toggles the 'chapters' check box. Which for some reason will rewrite the chapters with no audio. I had the same issue you did.
I now just check the few boxes I need and it works fine now from iTunes and my ATV