What does it mean if re-multiplexed MPEG files are smaller

[MrMungus]

than the original file? (e.g., from 350MB to 339MB)

I'm asking because these are files that I'm having a problem using in TMPGEnc DVD Author (produces DVDs with lost audio sync, presumably due to frame dropping during capture resulting in an MPEG-2 file that plays fine but doesn't work well for authoring).

Curious...and wondering if this fixes whatever was wrong with the original file...

[SatStorm]

It means that the padding is removed.
Nothing to worry about, except if you do VCD

It doesn't help when you have those problems with authoring applications. The faster way to overide it, is not to try to fix it: Detect the second the problem appears, and cut it out using programs like mpeg2vcr. Cut about half a sec and that's it. No problems. IMHO always....