Does ClamWin not find infected attachments in .eml files?
When I did a right click scan on an .eml file that had an infected .zip file attached it found nothing, while it did detect the infection when scanning the attached .zip file after saving it to disk.

you need to turn on "Treat files as mailboxes" setting in the advanced options. Please note that it will make scanning slower.

That did the trick, thanks very much.

Four files out of forty-two are infected, I knew something was wrong.