This is how it's supposed to work when you use imap.
Are the missing messages marked read? What view are you using? I'm thinking a filtered view is hiding them.
The emails are not marked read. I tested each view and checked that there are no filters. This problem started occurring several weeks ago on about fifteen different computers here on both Outlook 2007 and 2010 but not on Outlook 2013. No views or filters were changed.