wp-blog-header and bbPress

I am integrating bbPress 1.0 with my WP 2.8 site. I want to use the same header and navigation in bbPress as I have on the blog, so if I add more pages the bbPress navigation will be automatically updated.

I included wp-blog-header.php in the bbPress setup and customized the bbPress header.php in the theme folder, and it all looks and works great – except that none of the WP plugins are being called into the header. For instance I have a WP plugin that hides some pages in the menu, but in the bbPress header the pages are showing again.

Is there something else I need to do when using wp-blog-header.php to make it use the plugin functionality?