Fairfox: Until a fix is made - or somebody works out how - just be aware that if you create (...or find, obviously!) ogg files for Quake and the two mission packs it'll only play the files for the base game; that's because you have to place them inside the 'MUSIC' folder as opposed to id1/music, hipnotic/music and rogue/music. You can only have one set of 02.ogg (etc) in there, for example, and you can't 'tell' it to look elsewhere.
I've no doubt some clever users will figure out a way, but in the meantime place the oggs in that 'MUSIC' folder, rename _winmm.dll to winmm.dll, and there you go. Even GOG themselves didn't fix this with the original, fully intact original installer.
Or just play the DOS versions, I guess. Blergh. Or go with Quakespasm, etc!
I have the opposite problem running Quakespasm where I can get the music running fine for the mission packs, but not the original base game.