I had problems in the past trying to run Fetchmail to retrieve e-mails from POP accounts. At that time I switched to a Windows based solution and ran it directly on my Exchange server.
Well I've phased out Exchange so I went back to Fetchmail on my cyrus server. Still problems.
It's the latest version of Ubuntu, and it still has the same bug that I experienced two years ago. Sometimes it just decides there's something in the POP3 box that it doesn't like and ends up dying. It stops retrieving mail entirely.