Board Thread:Support Requests - Designing Your Wikia/@comment-5270307-20160705145554/@comment-3508553-20160727035155

This may have been set in the MediaWiki:Wikia.css or MediaWiki:Common.css on your wiki....

If not then it is a case of colors being to dark or too light for a color range, thus the change. The orange may be to "light" for a white to show up well, and so the ThemeDesigner auto contrasts, the reverse would be true for the blue, save, that it uses white because it contrasts better against the "dark" blue.