Just to be sure I understand, are you saying you've written a Favoites List to the scanner, but the scanner isn't scanning that Favorites List?
If that's the case, the first thing I'd do is confirm that the Favorites List is indeed in the scanner. You can verify this by Menu>Manage Favorites then scroll down to see if that Favorites List is there.
If it is, then I'd run through the "x36 Nothing to Scan checklist" and see if one or more things there isn't the culprit.
(You might not be seeing that "Nothing to Scan" message on the scanner. I suspect that's because you are scanning the Full Database, thus there is something to scan, but not necessarily exactly what you want).