On a new build of Ubuntu 15.10, whenever playing Prison Architect there was a constant crackling/popping over the top of the game music and effects.
The fix was quite simple but took me a while to find. So here it is in case you have the same problem.
Locate preferences.txt (on my machine in ~/.Prison Architect/preferences.txt), open it and change ‘SoundEnableDsp’ from ‘true’ to ‘false’. Reload the game if it was open at the time.
Let me know if that works for you!