codeigniter htaccess php instructions not working

In my php.ini i have disabled file upload globally:

file_uploads = Off

And i tried to enable file upload for my codeigniter site only. So i added to the .htaccess file the following:

php_flag file_uploads 1

And i made sure that AllowOverride is setup as follow in the apache config file :

<Directory /var/www/my_codeigniter_app/>
    Options Indexes FollowSymLinks MultiViews
    AllowOverride All
    Order allow,deny
    allow from all
</Directory>

However file upload is not working. It only works when i enable file upload globally.

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