I always do my mortise from the same face and maintain that during assy. I have some height differences even though I am not changing the setup other than on short members I use tight width and longer pieces I use medium width mortise. Sample test joint was flat, actual the short side is a little high. Sample process was same mortise width as actual. Can be sanded out, but ... is this due to the different mortise width. Has me stumped.
Thanks
Brian