You know in Terminator 3, when the Terminator goes shopping, there's a song "Dat Funky Man" playing out loud? When I play the compiled movie, the song is almost gone, very muted down somehow. I only hear it when the Terminator steps outside, but that's because the song's volume is cranked up in that part.
Could it be the case because when compiling the AC3 sound, it does something 27db (lowering the volume with 27 db or something like that, it's the default configuration of the surround sound in Vegas).