been having the same issue. how do i fix it?
waste-board and 20x20 extrusions are all too short in the y axis by 1/16 when the w-b is perfectly square.
the x end plates seem square to the x rails cuz they are brand new and i measured them to be exactly the same. however with the y plates disconnected from w-b and the gantry in the middle they relax to their natural position which means 39&7/16 in front and 39&3/4 in back… 
