sded,
Glad part of my info helped you, hope it also helps the op.
I also use TB with pop Gmail and 2 other pop mail servers, and 2 isp mail servers.
All work great and Avast scans all incoming (and outgoing) email. Maybe my TB proxy setting is redundant (I'll check that out), but I can see that all email is getting scanned as it is.
Basic email troubleshooting starts by checking these 3 settings areas:
1.) server and connection settings in email program (i.e. Thunderbird, Eudora, Outlook Express (eww), etc.)
2.) firewall settings and permissions
3.) connection and mail settings in A/V program (avast!,, naturally)
~Acco~
ps: disregard the info in my sig at present, it's outdated and can't be updated until I get at least 20 posts. Almost there,,,