Do you put him in a crate or x-pen when you leave or at night? He may equate coming with being put away & he doesn't want to be put away. That's what happened with Logan. Now that he has free rein he comes more completely, but sometimes he just doesn't want to be picked up or gotten a hold of if he's having too much fun being his independent self.
What worked for us when we need him to come all the way is: kneel on the floor, say come & point to a spot on the floor that you want him to come to, if he only come half way, say come here & point at the spot on the floor where you want him to be. When he hits this spot treat & praise.