Why not use mpeg2cut2? here: Mpg2Cut2
Works perfect for me. You can cut at keyframes, cut your recording "intro" and "outro" relult is still .ts (playable in MP always untill now). It can keep all your audiotracks. The result can be loaded in XMedia Recode XMedia Recode
(freeware) and transcoded into whatever you want (mkv with several audio tracks with aac, AC3 etc, divX, Xvid, iPod compatible stuff etc.).
This is my way, trying a lot of stuff (ProjectX, PVAStrumento, DVRPro, NeroRecode, TSRemux....) Simplest and best.
I use h.264 as video codec (2pass variable bitrate, with B-Frames) and AAC as audiocodec, mkv as container. It can keep pixel aspect ratio (like anamprh 16:9 movies), crop black bars (you can even decode cinamescope movies to 21:9 cutting bars and keeping anamprphic pixels) Superb quality!