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You can setup a user job to do the conversion. Create a script using your Mencoder commands, and use something like $1 as your input so you can easily feed the new files into it without having to hard code the new filename each time. mythrename.pl (IIRC) is the script that renames your files to give them meaningful names. In the end, to do what you are talking about, is probably easiest to do with nuvexport; it will do both the conversion and the renaming.
Also, why are you using that release? It's getting quite dated now, and I suspect 0.20 will be released shortly after the end of the "google SoC" summer ends. So at this point, you are nearly 2 releases behind. Your choice, just suggesting you may want to consider upgrading after the 0.20 release.
Distribution: Ubuntu, Debian, Various using VMWare
I will have a go at that when I get the chance.
I am using 0.18, because that is the version that is in the Ubuntu Dapper repositories. Do you know if it is possible to upgrade MythTV without losing all my channel settings (this was actually quite difficult to do, so I don't want to lose them)?
An upgrade to 0.19 (or if you wait for 0.20) probably won't screw up your channel settings. Although, I'd definitely burn a backup before trying just in case something really bad happens; or worse, you don't like 0.19/.20