Header Highlight Background Colour can be changed, but in order to achieve a unified look, I need to change Navigation Bar Highlight Background Colour as well (from default blue).
Sorry for the delayed reply. The look and feel customisations will be improved greatly in JIRA 6.0 (out in a few months). You could try and override the one in your instance by inspecting that menu item using the devtools in your browser (I'd recommend Chrome) and then override the style by placing the CSS overrides in the announcement banner.
in the Stylesheet of the wiki space (or Global Stylesheet). Works in Confluence 5.7 at least.
Alternatively, probably this is OK (in macros or the like):
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