Hmmm... it could be that hotmail doesn't completely follow the POP3 rules (Gmail has had that same problem).
Can you check with another POP3 email client and see how many emails it shows (eg: thunderbird)?
BTW: in Messenger does it also say +880 emails in the upper right corner on the mail icon?
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EDIT: I just tested it with an hotmail account myself, and it works like it should (read mails are not counted).