I think it's the switching from the 100 limit to 50 that is the real issue. Another report: http://forums.joeuser.com/342316
The addition thing has been a long standing issue.
Yeah the 50/100 thing is the bigger point. I noticed this quite some time ago but thought it was simply a site to site difference in PM limit. But landisaurus' post implied that the limit switched from 50 to 100 and back randomly on a single site and when I rechecked the results that I got when I made my first reply to his post it turned out I got different results even just a few minutes later.
The addition thing has been around forever but I think it's more of a subtraction thing. It's not something that happens all the time but I *think* if you "delete forever" directly out of your Inbox that always works reliably but if you "move to trash" and then delete, the message gets deleted but sometimes your message count isn't decremented. But as has been noted if you're willing to "empty all folders" then you do get reset back to zero.
I don't think anyone would complain if this somehow got fixed as well.