Did they merge the games together as a single file structure like they did with HL2? I don't have them installed since the change, but I could see that causing problems with the music.
opposing force's original soundtrack didn't work on the steam version so they just shoved in half-life's soundtrack. the pipeline update changed it to the original soundtreack
Gearbox hasn't changed the filenames for the new soundtracks in the Opposing Force files. I know it sounds stupid, but that's the reason why you don't hear Opposion Force music in the Steam version, the base GoldSource and HL content have priority over the Opposing Force content.