Navagon: I think it was always like that. It would be nice if it was fixed though. I don't see how things like that would interfere in GOG's plan of releasing games that play as they used to. I'm pretty sure the music cutting out isn't an intended feature.
Smannesman: I think that was introduced by changing from CD audio to whatever you want to call it audio.
Ah, yes, that makes sense.
I only ever played a demo of the game until the GOG release. Naturally that didn't have CD audio on it either. I'm fairly sure it had the same problem. Which is understandable as LA aren't going to be too fussed about a problem that doesn't affect the game proper.
So it seems like GOG used the demo way of doing things hoping that would be good enough. It wasn't.