I think I've researched this issue to high heaven and have found others with a similar problem, but I haven't found a solution that works.
As the title implies, I have a site with multiple gantry templates installed. The other templates are variations of the original template, and when I turn on SEO friendly URLs, the CSS for those templates does not show up. Instead, the pages are rendered with the home CSS.
I am using the .htaccess file and I've uncommented the RewriteBase rule as well as RewriteEngine On and commenting and uncommenting Options +FollowSymLinks has no effect.
Both Search Engine Friendly URLs and Use URL rewriting are turned on.
When I turn everything off, the CSS goes back to normal.