I have a pair of internal Exchange 2010 users who seem to be having junk mail issues. Both are running Outlook 2010. User A sends a message to User B. Almost every time, User B finds User A's message in his Junk Mail folder. Yes, there are times when User A's message comes directly to User B's inbox, as it should. User A has no rules set up in Outlook. He also has specifically right-clicked on a junk message from User A and selected "This is not spam". This does not seem to matter. He has also turned his JunkMail settings to the lowest possible. All messages from any other internal user come directly to this inbox. Also, when User A sends the same message to any other internal user, the message finds its way to the inbox of every recipient except User B.
On the Exchange side of things, no spam settings have been enabled for internal messages. I only have one Exchange 2010 server that does not filter internal messages.