If you are running a script such as mambo or joomla and use the script to install a template, module, etc. the script will take ownership of the file and you will not be able to delete it using ftp.

The only method to delete the file is to login to the script you used to install the file and use the scripts features to have it deleted or you can try using cPanel's File Manager. You can visit the scripts website or forum to find more details/guides about this issue.

These components will allow you to delete or edit these files:

Mambo - http://mamboxchange.com/projects/mamboxplorer/

Joomla - http://extensions.joomla.org/component/option,com_mtree/task,viewlink/link_id,102/Itemid,35/

WordPress - http://wordpress.org/support/topic/27582