At the moment im using the POP3 mail option on plus! to check the mail in my btinternet mail account. The thing is that instead of listing only the new emails (as it should) it is notifying me of every single email in my inbox! i.e. 123 new e-mail messages appears at the top.
Is there something i can do so that I only get the new email messages rather than every single one?

No. Many servers return the number of all emails, instead of just the unread ones. This is a limitation and Plus! (or you) cannot do anything to change this.

The only think I could recommend is that you make a folder in outlook express or whatever you use to read your e-mail called "Read". Whenever you have read an e-mail put it there, and put all your current read e-mails there as well...that way when Plus! notifies you of new e-mail it will be the new e-mail in your inbox...

ahh very clever