> But if you do want to leave them on the server, outlook flags it so that it knows not to retrieve multiple copies. Pegasus doesnt,
> meaning that every time it polls the server, it downloads another copy of the same messages to the inbox. I had 50 copies of the same
> email in my box!!

Biut Pegasus Mail does know how to do this.  Have you set Pegasus Mail to leave the mail on the server and to only download unread mail?

Download only unread mail  The usual practice when retrieving mail from a POP3 host is to delete it from the host when it is successfully downloaded. If you do not delete it, you would normally expect to see it again the next time you download mail from the host. Pegasus Mail incorporates a powerful and complicated facility which allows you to leave mail on the POP3 host without deleting it, but only download mail you haven't already seen. Because the POP3 protocol does not actually provide this facility, there are some limitations on this command, the most specific being that if you run Pegasus Mail on more than one machine, each one willhave a separate list of what you have already seen; so, if you download mail using one machine then access your account later from a different machine, you will probably get the mail you downloaded the first time again, where downloading the mail on the same machine you originally used would only show mail which had arrived since the last time you accessed your account. Check this control to instruct Pegasus Mail to attempt to download only mail you have not read. The effect of this control is probably meaningless if you do not also uncheck the "Delete retrieved mail on host" control. Using this feature can significantly increase the time it takes for Pegasus Mail to retrieve your new mail.

I'm troubled by the behavior of the mail server options.  On Outlook for example, when you choose to delete messages from the server after downloading pop3, you arent able to retrieve them subsequently from another email method (web based, alternate email program). Which is fine.

 But if you do want to leave them on the server, outlook flags it so that it knows not to retrieve multiple copies. Pegasus doesnt, meaning that every time it polls the server, it downloads another copy of the same messages to the inbox. I had 50 copies of the same email in my box!! 

 So, this is a bit of a flaw, in my view. Be nice if something could be done to make this option a better one :) Thanks so much.

Have you looked at the 'Download controls' tab where you set up the POP details?  There's various controls there that can do what you want.

I have to admit, the functionality is somewhat hidden, but it's certainly not a flaw. Go to Tools | Internet options | Receiving | Edit (select the pop host you want to edit) | Download controls, and then select Download only unread mail.

Edit: I hadn't finished writing my reply yet, Paul! :-)

Cheers!
Steffan