I have a really weird issue that just occurred on a client site.
I updated the permalink structure from /%category%/%postname%/ to /%postname%/ and suddenly my pages don't respect templates and are defaulting to index.php.
What else is strange is index.php is attempting to display the latest blog post of the site and not the actually page you are on, for example /about-us/ is not using template-about.php it is using index.php with the latest blog post content.
I have deleted and rebuilt the htaccess file, flushed the rewrite rules and nothing is happening.
If I set permalinks to Default(/?p=123) the site works just fine.
Does anyone have any ideas? I am at the end of this very large project and I have no idea what to do!