The problem seems most likely to be coming from your use of the Magee Shortcodes plugin. It is being used on the home page, but not the other ones.
Because of different levels of caching (the Customizer has its own settings cache, and doesn’t really save them until you exit the Customizer), there can be issues with keeping the Customizer in sync with the Legacy admin settings. I never use both at the same time. If I need to test something, I always publish and close the Customizer before trying Legacy settings.