From MozillaZine Knowledge Base
An incorrect new mail count under Tools is a Windows bug.
- If you have TweakUI, go to Repair > Repair Unread Mail Count and Click "Repair Now".
- If you don't have TweakUI, Start -> Run -> regedit, navigate to HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\UnreadMail\account and delete or modify the MessageCount values in the account sub-keys .
Because of this issue, this feature was removed in Firefox 2.0.