I have used comskip for years on mpeg files and on .ts files from my HD-PVR in SageTV. With some files I like to run comskip on the original file and then reencode them with Handbrake to mp4 to make them more portable for iDevices, etc. But at times in playback in Sage these files get in endless loops which I am guessing is caused by the time scale being marginally different in the processed .mp4 file vs the original .ts file. Therefore I would like to run comskip against my final file but when I try to do this is says that: