The quickest/easiest way to fix this is to mark every PM as read for that particular user. You'll need the userid and the current time in seconds, for example: 1213616430 is the current time.
update ubbt_PRIVATE_MESSAGE_USERS
set MESSAGE_LAST_READ='1213616430'
where USER_ID='#'
Replace # with the userid in question.
I tried that and it did not work for me?
So I when into ubbt_USER_PROFILE and edit my userID and edited USER_TOTAL_PM from 5 to 0 (after I removed all PM messages)
Looked to have worked or the world is about to blow up!