as Mr. Carius describes on his website http://www.msxfaq.de/clients/outlook2003e2010.htm (in german) there is a Problem that Outlook 2003 in online Mode displays SubFolders not only at their place but also on the root of the Mailbox. This only occurs if one has more than 3 hierarchy steps (for example Mailbox\f1\f2\f3\f4). (Mayby you have to start outlook with /restfolders to see this problem). Webmail and cachmode are not showing this error).
He describes that the beta of exchange 2010 SP1 has still this problem.
We have the problem too - i tried to move such a mailbox back to exchange 2003 - after that the Problem had been gone.
Does anybody has more information about this and is there a hofix from Microsoft?