Any more updates on this?
I've just tried downloading a new version of the FLAC OST on GOG, and the sound problems I identified with those two tracks (there may be more, I just haven't looked further) are still there.
The reason it has crossed my mind recently is that I have seen updates for another game on GOG (Stalker) where issues with the FLAC audio tracks were fixed, so thought I would update this post to get see if there has any progress remastering the FLAC soundtrack?
I have the impression that since nearly 2 years are past, this will never be fixed, but I thought I might as well try one last time, before giving up altogether.