I think the best you can do is download the version 4.5 Beta because it uses a new mail detection that will work automatically with Thunderbird.
Instructions here: http://forum.avast.com/index.php?board=11;action=display;threadid=8044
But you can try first, if you want, check your settings: avast! could scan just the unread messages (right click the ‘a’ blue icon > on-access protection > choose MS Outlook plugin at left and Customize at right > browse the settings and change what you need/want) 