I have seen the following symptoms with all combinations of the following Exchange Servers and Outlook Clients:
Exchange 2003, Exchange 2007
Outlook 2003, Outlook 2007, Outlook 2010
If I set auto archive on a series of folders or move the folders manually or use programmatic access to move items and/or folders to external PST files, some can get left behind and have to be manually copied. It's intermittent and if anything the programmatic access is the most reliable but none is failsafe.
Another example here is a Folder with a series of sub-folders after I have completed moving messages. There are no messages visible and yet overall folder size (including sub-folders) indicates 58kb spread in 6 or 7kb chunks amongst multiple sub-folders.
Sometimes when attempting a move I get a warning about unable to move due to Private Items present but then I go deeper into the folders and it works (on the same data) - uh!
This can occur when I am logged into Outlook as the owner, or as another user who then attaches to that mailbox with Full Access Privileges.