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Anyone any idea what it is doing, and how I can stop it doing it?
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Use "ps -efw | grep fetchmail" to get extend information in fetchmail's command line and look for a configuration file, usually, "/etc/fetchmailrc".
Read that file. It will show what accounts, what passwords and for what local account it is redirecting your messages.
I don't know what distro are you using. The most common way to stop a service is "/etc/init.d/fetchmail stop" and "chkconfig fetchmail off" to prevent it to run in next boot.
You may check your system logs to find why you are not getting your mail in. "grep fetchmail /var/log/messages" will show all fetchmail messages related.
cheers,