there are some tracks where I just want to get off some extra bits of crap not always related to the song, or to remove the long gaps for 'secret tracks' on some CDs.

Ah, yes, that will work, then.

If you can use GapKiller, or other MP3-splitting packages, you can split one of those secret-track files into three parts and discard the silent "middle" track. As long as you know the time-index markers.
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Tony Fabris