That is a bit strange, but may be down to the type of email, if in the outlook account settings some of those use SSL (secure encrypted) traffic then they may not be being scanned ?
Ah, that is it! I removed the SSL and TLS settings in outlook and Avast started working again.
I assume that when the Outlook Addin was working it was able to handle the virus scanning directly inside Outlook, but with out the addin working, then the SSL connection from outlook to the mail server meant Avast wouldn't be able to see the messages.
At least I feel safer now my emails are being checked.