I would try to search the forum for other threads... there have been a number of people with this issue...
Do the standard batt pull
If not fixed... make sure you have a backup on DM and then wipe the handheld and restore.
If you do not have a backup, then backup first, wipe, restore. I do not think the issue will live through the backup / restore process... but we will see
I usually wait for a new unread message to come up and when I'm in that I try to go to the Next Unread Message and it usually takes me to something I forgot or seems to help my phone reset itself. If that doesn't work then usually it goes away when I power down for a min and restart.
Posted from my CrackBerry at wapforums.crackberry.com
your message box isn't just for emails it will also show missed calls. and if you didn't set up your screen to seperate sms/mms from emails it will also show texts in you message box. You may want to check those areas too.