For me, when on a board and not in a post, the count displays the correct number of messages. It's a site issue. I opted as per Meatloaf to have my mailbox archived. I'm sure they will fix this issue in the near future.
BTW, why does the mailbox indicator at the top of the page sometimes show the number of messages and many times recently just shows 99+?
I've moved your 1200+ PM to your inbox archive. The newer style pages will show 99+ once you reach 100 or more while the older style pages don't. No PMs ever go away. Once you reply to a PM, unless you select "Keep", it goes into your inbox archive. The "Remove" option does the same for PMs you don't reply to. "File" will let you put PMs in folders if you wish.