vB totals your PMs from "the beginning" but usually will only show you the last 30 days' worth in your control panel (I think that's the default setting). Messages that you're "tracking" and any items in your "sent items" folders count towards your total as well. When you're in your PM control panel, make sure the left-hand corner says "show messages from the beginning." Then click on the "jump to folder" in the right-hand corner and check out what you've got stored in your "tracking" and "sent items" folders.
Wendy, I'm sorry you're having that problem, too. But now I know I'm not crazy. I've cleared out everything I possibly could short of deleting EVERYTHING; I have something like 28 messages total. Yet system keeps telling people my mailbox is full. Only mods have been able to PM me. I thought it might not be only a problem for me, and that's true.
In order to save space and keep our costs down there is a limit to the number of messages you can store. This total includes inbox messages, sent, tracking, and saved messages. So following Brie's instruction make sure you remove all unwanted message from each area.
Perhaps members are not aware that we are now allowed ONLY 15 pms TOTAL, between inbox, sent messages, and message tracking. The first thing you might want to do is turn off message tracking; otherwise you'll add 2 for every single message you thought you sent. Then, as has been suggested, go back to "the beginning" to see if you have some messages left from more than 60 days ago, and delete those golden oldies. Then you have to start praying to the system gods.
PS: I still don't know why the e-mail function has disappeared.