Uncheck "Leave a copy of message on server" in the advanced properties of the account. See http://support.earthlink.net/mu/1/psc/img/walkthroughs/windows_9x_nt/email/oe_6.0/7801.psc.html for a very clear instruction.
If your ISP offers a web-based interface to your mailbox ('webmail') you can use that to delete the messages you already have, in stead of receiving them two more times.
Hope this helps.
Until a few weeks ago I was running Windows 98SE and using OE6 quite happily to download messages from 3 pop3 and 2 webmail accounts. After encountering various difficulties which started with an error message about lack of memory, I ended up unable to even open up OE, nor could I open anything on the internet, so I assumed it was an IE problem and reinstalled W98. I seemed to be able to get online (i.e. modem dial-up working OK) but got "DNS or server error" messages when trying to access websites, and still nowhere with OE. So after 2 weeks I took the plunge and upgraded to Windows XP (Pro), and it all seems (touch wood) to be working properly, except ...
each time I open OE my waiting emails from my first pop3 account keep downloading, and as there are so many of them I time out before they're done or have moved onto the second or third account. When I reconnect they start downloading from scratch again (or from June 6 for some reason, so some of them have already downloaded 3 or 4 times!) - can anyone help me please? I can access my webmail accounts via the internet at least, but I really would like to get OE sorted as I have loads of rules set up, I have got used to it, and prefer all my emails to be together ...
p.s. sorry if some of the above is a bit long-winded/unnecessary :o(