You could try this:
http://www.videohelp.com/tools/H264TS-Cutter
or
http://www.videohelp.com/tools/TSSniper
or try to use PVAstrumento to remux the streams, although if ProjectX fails this might too.
You can cut MKV with
http://www.videohelp.com/tools/MKVtoolnix
or
http://www.videohelp.com/tools/SolveigMM-AVI-Trimmer
but I don't know if these can do frame exact editing.