DVD Player error 47

You could check out subler, it's a great .mp4 swiss army knife, and supports soft subtitles. I've used it with success with my Apple TV 2, and it work without issue, although I haven't tried on my iPad yet.

If you're using an Apple TV to play this content on the TV I share your pain, and the time to convert everything is also a pain! This is an alternative suggestion, not an answer to your question.

If your main goal here is to simply watch the content, and you'd prefer not to have to rip, then perhaps XBMC to simply view it may be a better option for you (it was for me).

I gave up transcoding everything months ago because of the problems you describe, the long time it took to do it, and all of the steps to get it from the PVR and disc initially into iTunes. I then found XBMC for Mac; it plays the vast majority of formats without the need to convert anything, and maintains it's own library created from wherever you store the files. Obviously it won't be in iTunes, but I don't see that as an issue as most of the content is transitory and I don't keep it for long.

If you do use an Apple TV, then you could airplay to it while running XBMC, or if you're daring, you could jailbreak the device and install XBMC on it and share the folder with the shows.