When Messenger Plus! asks for the number, pop3 servers report the total number of emails in inbox, not the number of unread ones. So neither you nor Messenger Plus! do something to fix this.
What you can do as a workaround is just creating a new folder at Yahoo mail as "Read Mails" and move mails to that folder after you read them.
There are some other threads about this case,
search the forum to find & read them.
quote:
I haven't a client like outlook to read my message, I read them on the yahoo site. Is this which done this problem ?
No, that doesn't cause this problem. However if you get a program like this, you can use that because it looks like your Yahoo! account supports POP3.
Windows Live Mail is a good one I think.