Originally suggested in a comment in this document: http://www.jivesoftware.com/community/docs/DOC-1110
In your theme try changing the include in the community.ftl
to be a relative path so your updated community-header.ftl that is also
in your theme will be loaded.
<#include 'include/community-header.ftl' />
Thanks. That's the conclusion one of our co-workers came to also.
That solved our problem.