Problem with url helper functions, SOMETIMES

[eluser]CroNiX[/eluser]
Im not sure whats going on but on some pages when I use url helpers like base_url(), site_url() and anchor() they don't seem to work properly on some pages.

in config.php:

Code:

config['base_url'] = 'http://www.mysite.com/appname/';

If I do

Code:

echo anchor('controller/method');

it creates http://www.mysite.com/appname/controller/method as the href, but when I click on it it goes to http://www.mysite.com/controller/method.

It works on some pages, but not others, so Im kind of confused.

Heres the .htaccess from www.mysite.com/appname

RewriteEngine On

# Handle the index.php file
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ index.php?/$1 [L]

I had to add the ? after index.php to get it working on the live server.

Any help would be appreciated.
Thanks!