The problem I was having with Thunderbird just started when I "upgraded" to Thunderbird 3.0.
The new version has some weird security settings, that don't seem to work correctly anyway!
After a lot of frustrations with 3.0, I gave up and reinstalled Thunderbird 2.0.0.23, and all my problems went away!
Including the scan note problem! I have now set my security (in Thunderbird for "TLS if available", and the notes show up!