Again - what you might have to do, if for instance you have 9 pics to join in a square 3X3 is (for the sake of argument):
open the top 3 pics individually, resize them so that they have the same vertical measurements.
go into panoramic - join the photos
save
do the same for the middle and other row
then join the top, middle and bottom together (will have to make sure that all the scanned images have the same wXh to avoid stretching).