Something here doesn't add up. Does the user receive these internal emails in his/her Exchange mailbox? If the emails are coming into the Exchange mailbox, then there's no reason they wouldn't be delivered to the Blackberry, unless there is some rule or policy that is preventing delivery of messages with the specific attributes of those messages. So in that case I'd advise looking at any rules or policies that are being applied either on the Blackberry server or on the user's Blackberry device.
If the messages are not being received in the Exchange mailbox, then that problem has nothing to do with the Blackberry device or the Blackberry server, but is an Exchange problem. Can you clarify?