Customizer.js changes not being recognized

It’s been a while since you wrote, but I was having the same problem and your question allowed me to solve it, so thank you! I was going crazy trying to figure it out. I am working from Underscores, as it looks like you are, and the fix was to change the script’s version number.

Where you enqueue your customizer.js script (near the bottom of inc/customizer.php in Underscores) change the version number to today’s date, or tomorrow’s, a la ‘20160215’. Mine was 20130508 previously, but once I changed it the current version of the script was loaded and my custom controls were affected by the JavaScript.