My only guess it's people replying to your posts and their post subsequently being removed. Or with that many PMs, are you scrolling all the way to the bottom to see if they were replies to your posts on the board?
I could be wrong, but I don't have any idea what it might be otherwise and haven't heard anyone else talk about that kind of glitch. You could always clear your cookies maybe.
And, moving some PMs to Archive isn't a bad idea. Depending on how many you actually have in your inbox, that could possibly be leading to some funky results. PMs are never deleted, they're just moved to an Archive tab so you can always access them later if needed.