Could you be seeing something similar to the phenomenon seen here:
2 Channels Performing Wrong Liquid Class - Hamilton (Venus) - Lab Automation Forums
If the plates/deck is not completely level (in the x direction in your case), maybe the pipette forms a partial seal with the bottom of the plate that resists the dispense in the final 1 or 2 columns. Do you still see the underdispense if you increase the pipette dispense height?