My colleague is having some difficulty with her Mail application, running under the newest version of OS X (Tabby? Tigger? Something like that). Basically, her Junk folder indicates that there are messages, but when she clicks on the folder, she’s unable to see them (to verify, for example, that there are no false positives).
I’m no Apple guru (I’m not the guru of any fruit, actually), and have a busy day, so I spent 90 seconds trying to debug and then had to move on. It’s a POP account, and I ran through all the Junk mail settings, and nothing jumped out at me. I took a quick screenshot, which does little other than prove I’m not making all this up. Any suggestions?
In exchange for your group expertise, let me offer you some random video of a goat (AVI). There’s no punchline or anything, just a goat on a table.
DarrenBarefoot.com 
So that’s what all my house parties have been missing: the goat on the table. Thanks, Darren.
(Can’t help with the Apple stuff, I use Windows/Linux)
does this help?
http://email.about.com/od/macosxmailtips/qt/et101104.htm
just a quick google.
armando
Awww, I want a goat now…
I had this problem a while ago as well, and it was driving me crazy, but I found the same info that Armando did (on the Apple web site): with the Junk folder selected, click the Mailbox menu and choose Rebuild. Poof!
She’ll do well to clear out the junk folder frequently, by the way. Mail’s tendency to get a little confused seems to increase the more items a folder contains.