WP isn’t using Template Files

This used to work but I can’t for the life of me figure out why this no longer works. I’ve tried disabling plugins and bringing them back one by one and then I tried to reinstall the WP files but still it won’t work. Basically, all of the tag pages and custom taxonomy pages default to the index.php template instead of the taxonomy.php template.

The other issue I’m having, and I only mention this because it might related, is that WordPress keeps throwing up 404 errors for any document in the theme or plugin that isn’t part of WordPress. For example, I was using a regular php document, that was stored in the theme folder as part of an ajax call. It kept throwing me 404 errors, when I moved it to root, it worked fine. This has happened with quite a few different files so it isn’t isolated. So any ideas why this is happening? Thanks.