This sounds similar to a situation I encountered awhile back.
It was an OE email. When it was downloaded, it was detected. I used the delete button, the same email was detected, used delete button, recieved message that avast couldn't find the file(something like that, the exact message is in an old post some where), chosing no action allowed the download to continue. It did this with at least 2 more messages that night. Now upon reflection , I am sure the infected attachment was stripped off when the where placed in the inbox. And no, they where not duplicate emails, I only recieved half of what was detected. ie 6 where detected, in fact there was only 3.
Maybe there is a small bug under certain conditions?