I havent used this software before but just reading about it at _http://moonlight.co.il/products/Xmux.shtml
I have basically been doing the same as it does but use TMPGEnc to D-mux the MPEG2 file and re-mux with Wombbles MPEG2VCR or with M2-Edit. Source for both have been posted here before, use Search button to find.
I'll d/l xmuxer myself and try it out as well.