[Plugin: Custom Permalinks] Always worked, now takes out template

I have always loved this plugin and have it on a dozen sites. The new site was perfect until I made the move to the live site (site is in a subdirectory, same as all my other sites).

The home page, blog home page and single blog post pages all work fine. All the interior pages load the content, but can’t find the css, header, footer and sidebar files. All pages in the site use the same template page.

When I disable the plugin, it all works fine, no matter where I have the WP permalink settings. With the plugin activated, I lose all styling and includes for all but the pages listed above.

Unfortunately, I need specific URLs for this site, as it has been around for a long time, and there is no structure in WP permalinks that will work.

Any suggestions much appreciated. I am in panic mode.

http://wordpress.org/extend/plugins/custom-permalinks/