Pages within section not showing section theme

My main site has one theme and I created a section that will have a second theme. This worked when I was specifying the pages in the section manually (listing paths in the "block visibility" field). Due to design needs, I've switched to a PHP code based visibility setting. The section is still being applied to the pages properly (the section is listed in the body tag's class attribute), but it's still using the main site's theme. What could be causing this? Is there a mistaken setting somewhere?