The SMTP Namespaces tab on the properties of the Exchange Organization contains the namespaces in question, as a result, they will be counted as Internal in the Reports.
The first is through user entry. This is done using the Organization Property Page, Internal Namespaces. In this property page, the user can add any number of Internal namespaces they want to categorize as Internal.
The second way this is setup is through two gatherings that are done in MessageStats.
The first gathering is the Internal Namespace gathering that is done at an Exchange organization level.
This gathering goes out and looks at any and all SMTP Recipient Policies in place and extracts out the domain and adds it to the list.
The idea is that if there is a policy for a given SMTP domain, chances are the domain is an internal address.
The second gathering is the Mailbox gathering. When this gathering is looking at the main SMTP address for the mailbox as well as the additional SMTP address, it takes all of these domains and adds them to the list.
The idea here is that if there is a SMTP address for a given mailbox, then it should be considered Internal.
Given the Internal Namespace list, MessageStats checks the given address domain against it and sees if the item is in the list. If so, the address is considered Internal. If not, the address is considered External.
An example may help highlight this further. Let us assume that a given mailbox is sent a message to four recipients.
Three of which are other mailboxes in the company and the final one is an SMTP address of the given person's Friend. Assuming that the SMTP address of the Friend is not part of the Internal Namespace list, MessageStats would count this as 3 Internal messages and 1 External message.
This answers the question if someone emails from an internal namespace to an external namespace, 1 Internal message would be counted in the reports, with 1 External message counted
RESOLUTION 1
If they were manually added, remove the unwanted namespaces and allow the gathering to re-run.
Upgrade to MessageStats 7.5 and Download and install the attached hotfix. The following hotfix allows for the list to be manually maintained. All namespaces that were autodiscovered will need to be selected if you wish to have them reported as internal
