Using TMPEGEnc's multiplex and de-multiplex tools with an Mpeg2 file containing AC3 works fine.
Even though I think TMPEGEnc dosn't support AC3, it will split it or multiplex it fine.

But when using Merge and cut to edit an Mpeg2, the resulting new file has no sound. Loading this new file into the multiplex window confirms that there is no audio track.

Is there a way around this, or can someone suggest an editor that can handle AC3?