I have no idea what's the cause of this, but I'm just hoping that this issue has been reported already so you can link me to it so I can vote on it. If not, I think my luck is out.
So, I was in the middle of updating one of my maps to 1.10, and in one of the playtests, I noticed after a scene that featured a bunch of sounds and being played (and pretty much coincidentally they were perfectly timed with some of the random environment sounds and the music), and after the scene, all the custom sounds that were in the resource pack stopped working. The regular sounds from Minecraft still worked and the resource pack was still on and working just fine, but all the custom sounds didn't work. I even tried using /playsound but it didn't work either. It wasn't like this before the scene. Once I opened the map's backup the custom sounds were working again. I checked on the command blocks that played the scene to see if maybe it was an issue in the redstone but I couldn't find anything.