How to covert files downloaded by torrent with handbrake?

I use handbrake to convert files (generally into mp4) but I can't covert files downloaded from a torrent by handbrake. It says "Your source may be copy protected, badly mastered, or in a format which Handbrake does not support". I know it is not the last one because handbrake can covert avi and other file formats before but it doesn't work when it is from a torrent. What is the problem? If you can't find a solution, are there any other good converters that will convert torrents, especially into mp4 so I could use it i ITunes and on my iphone?

Try 'Any Video Converter'

If the torrent has stopped seeding, try moving a copy of the file to a new location and try again. If that doesn't work, maybe finding another copy of the movie in another format may help you out.

If the torrent videos you downloaded are pretected or have bad track, I think you can't use the handbrake to convert them. Handbrake doesn't handle DTS audio tracks or single VOB files. If you have a DVD-ROM with random video files saved on it (AVI, MPG, WMV, MOV, etc), Handbrake won't be able to convert these files. You may get ifunia video converter to have a try, I read an article "How to Download & Play Torrent Movies on Mac", suppose you have a Mac, and if the converted videos can be played on Mac, then you could transfer them to iTunes and play on your iPhone.