After I upgraded to Xubuntu 12.04 from 11.10, I noticed skype was uninstalled, so I reinstalled it with aptitude. Now if I install skype I don't have sound any more in my mp4 clips.
If I uninstall skype I have sound again in my mp4 clips, unless I pause the clip and resume, then the sound is gone again.
I tested this on parole and vlc. Is there a fix or is it just a bug?