I've had the same problem, but I don't know of a program that makes this job easy. But if you doubleclick on your original file in ProjectX before demuxing it, a new window will open (at least it does with .TS-files). There you're able to select which part of the movie to demux. Select all parts that you want to keep, just like you would have done in Mpeg2Schnitt, but ProjectX will cut the subtitle file too. Maybe it's a bit inaccurate, but it will save you some time..