L/R margin settings that apply to Headers cannot differ from those applied to the body text. If the Header isn't centering above the text it has to be due to an intentional or accidental layout modification [such as indentation or tabs] applied to one or
the other.
Exactly how are you imposing what you describe in your opening paragraph? Are you using the features of
Format> Document> Margins or are you making some sort of manual adjustment in the document, itself? If the former, what specific settings are you using?
What is indicated by the Ruler when in the text? When in the Header?
The settings shown here:
automatically provide the result shown here;
Notice that the Header is properly centered above the body text on both the recto & verso page.