Maybe the Junk folder isn't updated unless you select (open) it. Right-click the folder, Properties, and see if 'When getting new messages....' is checked. If it isn't, does checking the box make the count update when the Inbox is retrieved?

Thanks sfhowes, that did the trick. I have never had to do that for that folder before so I wonder if that is new from one of the updates. The minute i clicked that box and saved, the count populated for the folder. I did not know there was mail there before that.