Hi jbp
Since version 3.1.0.14 which was released a couple of days ago via Smart Update, POP email scanning has been working for me with both OE and Thunderbird.
There is a known bug in OE (which occurs with other AV programs as well) whereby the 'tag', in the case of PCTAV being:
"No virus found in this incoming message
Checked by PC Tools AntiVirus (3.1.0.14 - 9.066.002).
http://www.pctools.com/anti-virus/"
is seemingly arbitrarily added to the message as an attachment, but in these cases the actual message is still there.
What email client are you using?
Online manual is at:
http://www.pctools.com/anti-virus/help/ but it doesn't have much email troubleshooting info.
Pete