Don't know about BES, but I've seen this through BIS, and it appears as though it's tied to some sort of Exchange processing/maintenance. For a while, whenever my colleague updated the spam definitions on the Exchange Server, messages from the past would appear as new on the devices (this includes BlackBerry and Windows Mobile, so I don't think it's necessarily a BlackBerry issue). In doing some really brief research, the only thing I could really find was a suggestion that the Exchange Server was changing the message ID of these messages, so the devices (or BES/BIS) were classifying them as new and showing/shoving them.