The header settings weren’t applied because the header builder at the top option was checked.
I see all options are there normally. What exactly you don’t see?
As an alternative, we have developer a Header Builder that is more flexible and much organized than building using Theme Options. Here is a quick guide for it http://docs.creiden.com/circleflip/header-builder/
You can try it and let me know if you needed any help. Don’t forget to re-check the Header builder option in the Theme Options and select the default header to be rendered on the website.