The problem with Message Alerts is related to spam activity. Lately, there has been an increase in spam on pku.com. As soon as such activity comes to our notice, we delete the user account and all related activity on pku.com, including personal messages. However, the message alerts reside on individual user accounts and therefore we cannot modify it.
The reason your alert count does not match the Inbox message count is because some of the messages you received were spams, and the message has been deleted.
We are working on a fix and will notify you as soon as it is implemented. In the interim, we appreciate your understanding as we strive to keep pku.com spam free.