Are you getting doubles of all new email or just the replies?
Are you getting the doubles in the same inbox or they are showing up in the inbox of both configurations?
It sounds like you created two profiles that are using pop3 to check the same incoming mail server but you used different Email Address: and Reply Address: values for the different profiles so you could send as either one?
Does your email provider support IMAP? I'm wondering if the original solution was to configure your accounts as IMAP and not POP accounts. If you are not sure if you can do IMAP what is the domain name for your email address? If you setup IMAP configurations then you can connect from multiple mail programs and even different computers. They would all share the same view of your inbox and folders on the email providers mail servers.
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