You're right, it was changed in the CSS of your theme in the stylesheet.css.liquid. Once you change the HTML directly, it takes out the small piece of code that links it to the header color in settings.
I changed the header to #bb8b8b, the colour you had saved in the Customize Theme area. If you ever need to change it, head to your stylesheet (linked above) and change line 1141. :)
|a minute ago|