How to get Uploadify working with Codeigniter + CSRF?
Use this code, it enables you to define an array of controller methods that are not subject to CSRF: https://github.com/EllisLab/CodeIgniter/pull/236.
The issue is that Uploadify uses a Flash object, which is like a completely different browser, with different session, so the CSRF won't match your session if you POST the cookie data.
You would need to override the original CSRF function with a MY_Security.php file and make so you can get around it by, in example, sending your entire session cookie via POST and make so the CSRF can read it, so you can be matched.
You might as well try HTML5 uploaders like https://github.com/blueimp/jQuery-File-Upload that at least gives you a better chance at not having to do such overrides.