All my controllers are being called twice.

[eluser]WanWizard[/eluser]
This can happen if there is another element on the page (p.e. an image) that gets rewritten to index.php.

Use firebug's 'net' option to see what requests go to your server after you've requested the page, and see if there's something out of the ordinary (like an image URL not starting with assets or captcha). You could also enable rewrite logging (requires access to httpd.conf) to check the rewrite requests.