I've been running into this issue more often lately as more and more files come with lots of subtitles. My direct play on my TV causes most embedded subtitles to be transcoded. On larger movies this can be a problem maxing out my CPU. So I created a script that I put in my /usr/bin to pull out the subtitles. Figured I'd share for anyone else interested. Mine pulls out English and Russian, but can easily be changed to do any other languages. Script is set to run from the movies folder and will in