Just use the Submux program that comes with Vobsub. However if you try to use it in combination with Nandub muxing anything then it won't work, coz Nandub will mess up your file. Nandub is really good at messing up files
Did you check in the .idx file if the timecode for your subtitles are correct? If they only go to about 30 mins that would expain why the subtitles stopped after a while.