This forum is wrapped inside the WordPress theme to keep the style consistent across the site. To do that I included the WordPress blog-header.php file because I needed to be able to use the sidebar widgets even though the forum software is technically running separately.
I noticed a major problem though. Even though the forum pages are displaying correctly, the server is returning a 404 header so search engines think the page isn't there. I know the reason is because I'm including that blog-header.php file and WordPress thinks the forum page doesn't exist. But I'm looking for a solution to what seems to be a fairly significant problem.
And I did find a WordPress plugin that overrides the 404 header by sending a 200 header later, but that seems like it would cause even the correctly sent 404s to be overridden as well and that doesn't do any good.