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.
Fast Forward to yesterday and I find out that it this problem has resurfaced. Unfortunately, my previous solution was several months ago and I don’t remember the mechanism I used then. Additionally given that the problem resurfaced, whatever I used previously clearly no longer works. This meant I had to try and surmise the culprit (App Nap) and fix it again. So for future reference, the solution is to execute:
defaults write NSGlobalDomain NSAppSleepDisabled -bool YES
After this, you must restart any application that you do not want to be completely starved of CPU while in the background.
Hopefully this is useful for others out there.