I've confirmed this on my install, I have tried uninstalling it, and reisntalling it. It only monitors one of my smtp servers, and the other doesn't even get looked at by the mail scanner.
I noticed in the headers Avast adds some information, so I used this for testing.
On the account with the smtp server that is being monitored I get these headers:
X-Antivirus: avast! (VPS 0450-0, 12/06/2004), Outbound message
X-Antivirus-Status: Clean
X-Antivirus: avast! (VPS 0450-0, 12/06/2004), Inbound message
X-Antivirus-Status: Clean
On the account with the other smtp I only get the "Inbound message" headers:
X-Antivirus: avast! (VPS 0450-0, 12/06/2004), Inbound message
X-Antivirus-Status: Clean
Is this a limitation of your software, or something left behind that your uninstall didn't get? I am running 4.5 with all the current updates.