Converting DVD Deleted Scenes to MP4 - Subtitles Don't Match

[rickydavao]

Sorry, guys ... best title I could think of. This is something that has been bugging me for some time, even though it doesn't happen often. I back-up my DVD's to hard drive to stream to media players around the house, such as my kids' XBox 360. My daughter especially likes to watch the extras, such as gag reels and deleted scenes, so I often rip and convert those too. To determine what to rip, I usually select the "Play All" feature, note the duration time, and use DVD Fab HD Decrypter in movie mode to rip the appropriate feature.
After encoding, I have noticed that in some cases, while the audio and video (and closed captions if available) all match up nicely, the DVD subs (extracted via VSRip for example) and the chapter points do not. Also, when playing the converted MP4, the order of scenes is usually different than that from the original DVD. I'm guessing that this is because the associated IFO file has instructions to play the segments of the VOB file(s) in a particular order, which is ignored when encoding since the software I'm suing (StaxRip) only looks at the VOB file(s). I hope this makes sense.
My question is, is there a piece of software that can modify either the VOB files or the IFO file so that everything matches up after conversion? I can manually edit the chapter and idx/sub files visually to match up with the encoded MP4, but it's really tedious. Just wondering (and hoping) if there's an easier way. Thanks!

[Baldrick]

Try handbrake instead. Be sure to select to open the dvd folder instead of the vobs. And see if you can select correct title.