Sorry, we noticed that active color in the Header Builder related to the one-page websites is not included in the source code - for now we do not have any workaround to fix that because it's not attaching the 'active' class, so we cannot catch it any way through your website - you have to wait for the update which will add that functionality and even much more possibilities to create your own header.
For now, all that we can suggest is not to use the Muffin Header Builder, but our default, prebuilt headers from Theme Options > Header & Subheader > Header
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