Thanks for the tip on removing the if block. So, perhaps the regular expression is off? Basically, the rewrite-rule should fire if the url does NOT contain a period.

Examples:

/some/path //should hit the rewrite rule
/file.php //should NOT hit the rewrite rule

Here is php.conf as well:

location ~\.php {
try_files $uri =404;
fastcgi_index index.php;
fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
fastcgi_intercept_errors on;
fastcgi_pass 127.0.0.1:9000;
include /etc/nginx/fastcgi_params;
}