Where possible I would avoid using POP3 accounts. My host allowed me to upgrade to IMAP and it is so much easier. I think the only way to accurately create any form of mail client with POP3 is to download the messages into an SQL database which is a big task to start with, considering the IMAP standards have the functionality we need built in.
I experimented with flag setting in POP3 and it seems they do not stick at all, and it is almost impossible to retrieve the number of unread messages (ie. the Seen / Unseen thing does not work)
Converted to IMAP and it's working - the majority of the functions in this section seem to be IMAP focussed and WILL NOT generally work with POP3