Also, if you cropped a first image, say, then any 
subsequent scans work from that cropped size, 
until you close the scanning software program. It 
pays to cancel/clear (whatever your type of 
scanner software calls it) the scanning bed 
between images.  That way each image works from 
the full bed.  

Also check your scanning default preferences, and 
make sure they indicate you have the whole scan-
bed as your default.  I know some software has 
the option to concentrate on image areas 
preferentially.