Fix timecode in merged vobs
Libav has the tool avconv, which allows you to do that with the video filter setpts=PTS-STARTPTS.

I haven't tried this, but the following should do the trick for you:

avconv -i in.vob -vf 'setpts=PTS-STARTPTS' -c:a copy -c:v copy out.vob


For more information you can check out http://manpages.ubuntu.com/manpages/precise/man1/avconv.1.html