We have a custom WP content filter in place which essentially takes the post and makes changes to the content with reformatting a few things. With the WordPress SEO plugin activated, the content that we're modifying appears in the HTML <head> tag as if WordPress SEO is doing something which is triggering the plugin we have. With the SEO plugin off, it works as it should. With the SEO plugin on, its including a copy of the modified content in the head.
Any idea what might be causing this or how we can have our plugin modify the content after WordPress SEO?