If I understand correctly, you convert tivo files to Mp4s for your iPod, but the converted files won't play on the 360? I don't have a 360 so I'm not sure what codec it needs, but I do know that Tivo files have a 'wrapper' that prevents the files from being used by most editors.
I use a program called Direct Show Dump to 'unwrap' the Tivo file and make a regular mpeg that I can work with on any device. You might be able to use this procedure to transcode between the tivo file and a compatible 360 file.
For the last several months I've really been enjoying Tivo Desktop and it's converter for my video ipod. My main purpose for this has been that I'm currently living out of my house and my fiance's house. We use the ipod video cable to watch our shows wherever we are.
Recently, we moved in together and I thought wouldn't it be great if I was able to setup an external hard drive connect it to my 360 and not have to deal with syncing the ipod whenever we wanted to watch something. Itunes is quite annoying to deal with. Especially since the 360 supports the mp4 format now.
Everything has been great except that the 360 will not play any mp4 files converted by Tivo Desktop. I have used several free converters to convert all kinds of media into mp4 format and they all work fine on the 360. All the mp4 files will work in itunes, and sync just fine with the ipod. However, the ipod only has a 160gig hardrive and now we've gotten hooked on the idea of having all of our media at our fingertips without having to sync the ipod everytime.
Does anyone have any suggestions as to how I can get the Tivo converted mp4 files to play on the 360? Thanks for any help, and sorry for being so long winded! I guess it comes from listening to the show of indeterminate length.