The Email Checker seems to be showing me that there's new mail in my Yahoo account. I have 23 piece of mail in my Inbox. All which have been read. Yet, the Email Check still shows 23 piece of new unread mail. Is there a way for it to only indicate that there is 'New' unread email waiting in the inbox?

From the application's FAQ:

Q) The Email Checker is displaying the wrong number of messages?

A) The Email Checker is not a full blown email client. The Email Checker simply asks the server how many messages are pending retrieval, and, if there are any, that's what it reports. It also keeps a counter of the number of messages in the server so it will only notify you again when more mail arrives. The notification, however, will tell you the total number of messages still in the server, not the number of messages that arrived between the new and previous notifications.

This counter is reset when the number of messages in the server is less than the value in the counter (which means mail has been retrieved in the mean time) or when you tell the Checker to launch the email client.

The Email Checker has no way of knowing which messages have already been read but left on the server.

This said, if you manage to connect to Yahoo via IMAP instead of POP3, you might pull this off, since the IMAP protocol supports sending the number of unread messages.