For what it's worth, that's happened to me, though since the total number stays consistent (ie, 100 PMs, 1 New stays as 100 PMs, 1 New after I've read it, but would be 101 PMs, 2 New if a new one came in) I've never found it overly confusing. This has been true over Safari, Chrome, and Firefox. I thought it just happened to everyone.
It's also not an issue with the number of PMs you have. It's happened to me since long before I got up to higher numbers. What number specifically I couldn't say.