Not sure how to resolve this. However, the explanation is straightforward. If a message for a group is received, the Service Router handles the message twice (once to expand the group into users, and once to route to the users). The Archiver will probably need to check the unique message ID's before archiving it, similar to the way Local Delivery manages this.
If you can reliably reproduce this, I would suggest contacting Scalix Support, or opening a report in Scalix Bugzilla.