Won't add any php files to sitemap, only PDF

I scanned my website many times and even started a new project but I can't get this product to add any php files to my sitemap.xml.

The "Analyze Website Data" tab shows everything properly but when I build the sitemaps, they are missing all my pages and only contain my pdf files.

I am not using any filters.  I have never seen it do this before.

I have tried uninstalling and reinstalling but still get the same results.

The website I am trying to build the XML file for is www.portlandfellowship.com

This issue was resolved over email where the problem was cused by the user using canonical tag pointing them to the domain.

Relevant help entries:

http://www.microsystools.com/products/sitemap-generator/help/sitemap-robots-noindex-nofollow/

http://www.microsystools.com/products/sitemap-generator/help/duplicate-content-page-urls/

http://googlewebmastercentral.blogspot.dk/2009/02/specify-your-canonical.html