I know how to fix the problem (At least until the Techs can figure out the cause) .
However many New Messages you have in the negative, for example I had -8 New Messages, Send yourself a PM
by clicking on your username, (I just wrote Subject: Hello and the Message: Hello again) then answer it.
After you have answered your own PM, delete the original one, and your Negative count will go down.
Repeat for each Negative New Message.