One other thing that tkamiya's post has reminded me of. Check the movement in the enlarger bellows.There should be a screw that allows you to tighten the bellows so after focusing they don't move. Movement can be a problem if the print size means that the bellows are tightly compressed. I have had this problem with my Durst 605 and need to tighten the screw so that focusing knob is stiff to move.
It is possible that you correctly focus with each focuser then the bellows move slightly before you expose. In the case of the eye-balled print, was this the last print to be made? If it was and you focused by eye then instantly hit the expose button the bellows might not have had a chance of moving so that one was the best.
Just a thought