Just completed a migration from Exchange on SBS 2003 to Exchange 2010 on Server 2008 R2. Mostly this has gone well, mail flow is not an issue as far as the server is concerned. However, the Outlook clients need to have all their folders and subfolders manually updated by going to the send/receive tab and clicking update folder (even the inbox).
I've disabled cached mode as a work around but this has lead to a lot of spam appearing in the user's mailboxes as we had previously used the outlook clients to manage the user's spam.
Exchange is using a 3rd party pop connector to download mail from the company's hosting provider, but with cache mode disabled there is no delay from the time I force the pop3 downloader to retrieve the mail to when it appears in their mailboxes. so the problem seems to be something to do with exchange and the outlook clients.