I've modified my soundmunge.bat with the 'stub line, however the outputted sound.lvl file does not appear to contain the correct data for stock sounds. In particular, I'm after the TIE Fighter sounds which aren't being loaded.
Hmmmm. So that's where it was coming from, I was quite surprised to see that on some maps such as Dune See the sounds seemed to conflict with my custom loaded ones.
The instructions I'm following about the -stub line being inserted into soundmunge.bat are ones psych0fred posted. TBH I've never gotten 'missing' sounds working alongside custom sounds. Sereja has done it, though I'm not sure how as his assets don't include his mungers.