What version of SmarterMail are you running? My personal server is on 9448 (11/13) and I don't see this issue: I only see 1 copy of each message. That said, as SmarterMail archives at the spool level, I can see where you may see duplicates if a message is sent to an alias and to a user directly since they are part of the alias and the message is delivered to their inbox. So, my guess is this is expected behavior as we've not had any Archiving changes/fixes that would cause or resolve this behavior.
Derek Curtis
COO
SmarterTools Inc.
www.smartertools.com