One of us is confused....
I have no idea what your operating system is but you should not (unless there's no other way) be running cron through the web server. If you have command line access then run it as a normal cron script. However, it's important that you run as the same (operating system) user as the web server or you will definitely hit problems with file permissions. None of this is anything to do with Moodle users.
I have no idea what your operating system is but you should not (unless there's no other way) be running cron through the web server. If you have command line access then run it as a normal cron script. However, it's important that you run as the same (operating system) user as the web server or you will definitely hit problems with file permissions. None of this is anything to do with Moodle users.