We are setup with our SM server behind a Physical Box that does anti-spam and anti-virus filtering.
For this to work properly I have constructed automated processes that program both my SM server (adding domains, mailboxes, aliases, forwards, etc) and the AS/AV box (which also requires each account to be setup there).
The problem I see from time to time is if I program the aliases for a mailbox into both the AS/AV box AND into the SM box, it seems SM can get confused as to what to do with the messages when it receives it.
Sometimes it delivers it straight away, other times it can seemingly spin off into the ether never to be heard from again. (Even though the incoming message appears in the Message archive, it can end up never getting to the mailbox it should have been destined for nor does it seem to appear in an error lists of any sort).
If I only setup the mailboxes in the AS/AV server (no alias info, setup each alias as a mailbox there instead) and then only have the aliasing on the SM server, all these issues go away and things deliver exactly as I would expect them to.
I'm thinking this must have something to do with header modifications being performed by the AV/AS box and then SM trying to sort that out... but that is just a raw guess on my part.