Not sure what you're talking about. I watched the video you linked and there is NO background music, just crowd sound effects. In any case, the music in BG2 is intermittent on purpose, it only plays every so often. I doubt anything is wrong with your install.
I guess I forget to ask you to tune the volume up before you play that video.
Well I am quite sure that particular bgm would play every time after Irenicus says his first or second line, if tob is not installed. But just now I don't have a copy of soa only installation, so yes, I can't one hundred percent confirm that it's tob's fault.
Anyway I just give a try to ask it here. Perhaps I am the only one that are paranoid enough to notice things like this, because not even the g3 fixpack has fix this.