Commend Line PHP

I have a script which runs perfectly through a browser but when I try and run the same script at the command line (Fedora8, Apache)it stops due to permission problems. I have even tried running it as a root user, but still no success. Does anyone have any idea where I should look to resolve this? Essentially the script retrieves data from a remote ftp server and copies it to the local server. I want to try and run this as a daily 'cron' job.

Any help will be gratefully received.

Thanks