In one of the El Capitan updates, I had issues where iTunes playback would start skipping when the CPU was under heavy load. I noticed that if I brought iTunes to the foreground, the skipping stopped, but if the heavy CPU load application was in the foreground, it resumed. Being a developer, this meant that my music would continually skip whenever I compiled something, which is a common occurrence. I was able to conclude that App Nap was the culprit and disabled it.