If you know how to edit the registry, you can reset the counter.
It is in HKEY_CURRENT_USER\SOFTWARE\MICROSOFT\WINDOWS\Current Version\UnreadMail
Then you need to select the e-mail address that it says their is a new message for...
Eg: nospam @ test .com
Then in the right pane, it should have Message Count
Then right click on MessageCount, a box will pop up with the value: 1 inside.
Change this to: 0
Then click ok, and close the registry editor.
Restart, and walla.