CSS Folder in the Application Folder

[eluser]Aken[/eluser]
You should restructure your applications so that you are not intermingling logic code with static assets.

Code:

ROOT
-- pso/
---- application/
---- assets/
---- index.php
-- another_app/
---- application/
---- assets/
---- index.php

That way, the default .htaccess provided with CI will not interfere with your application functioning properly. You can then add your own .htaccess files for removing index.php in the manner you'd prefer.