This has probably nothing todo with Plus! directly.
Check you registry...
First check:
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\UnreadMail\your@mail\MessageCount
Make sure that the value of
MessageCount is
0.
Then make sure that the following Plus! keys also have value
0:
HKEY_CURRENT_USER\Software\Patchou\MsgPlus2\your@email.com\Preferences\POPAddHotmail
(If false (0), the count of unread emails in your Hotmail account is not added to the count of unread pop3 emails.)
HKEY_CURRENT_USER\Software\Patchou\MsgPlus2\your@email.com\Preferences\UpdateWindowsEmailCount
(If false (0), the count of unread emails in your POP3 accounts is not displayed in the welcome screen of Windows XP.)
See:
http://shoutbox.menthix.net/showthread.php?tid=21770&pid=205351#pid205351 pruned
and
http://www.msgplus.net/help_registry.php
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