I’m assuming you are referring to the customizer? Since WP 3.9, a lot of people are experiencing issues with 3.9 and it looks like they should have kept testing it before going full public release. One of the problems is the WP Customizer getting affected. I’ve even seen some people post compatibility issues with some plugins. You may want to inform WordPress about your colour selector not working properly because this sounds like another bug with 3.9
Your last question….is this in relation to what you are experiencing after you upgraded?