Not getting done automatically is a cron problem, not a conversion problem. Secondly, the change only applies to certain versions of mplayer. In some of the older versions of mplayer, you have to specify that the video does not contain b-frames (b-frames will cause mplayer to not convert a video at all). Some of the newer versions do not require this switch. However, this is server OS specific because I have seen that the same version of mplayer installed on different OS's behave differently. For example, on a CentOS/Fedora install, I have to certify the b-frames on the latest version of mplayer. However, on an Ubuntu install, I had to use the other code.

For the record, the default installation of vShare has both codes in the file: one is the first code with the b-frame declaration (commented out), the other is the code without it.