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Im looking for a way to transcode all/some of my videos using another video as a template......

I have a couple movies that play perfect on my TV and then some dont at all. I want to change them so they all play.

Is this possible?

Better to figure out why they don't play. Post ffmpeg output for them and debug log of play attempt. See my sig for how.

Most of play. Just a lot of them skip. Or audio not synced.

Try remuxing them first - a lot less time/processor consuming than transcoding and often fixes time code issues (particularly on AVI's). Either use WinHelper (see signature) to remux to the same container, or do it manually using ffmpeg:

ffmpeg -i sourcefile.avi -c copy -map 0 destfile.avi

(make sure the extension type remains the same - .avi in the above example, but modify for your needs). If this doesn't work, send through ffmpeg details as per jhb50's post.

If you still need this you may try using the directTV DVR (as I heard it supposedly transcodes everything). Still not sure that's the best solution...

While you can easily change the behavior of transcode-video to generate MP4 format with a command line option, it's sometimes handy to convert between formats quickly without re-transcoding.