Check the encoder wheel and see that it isn't spinning slightly on the ball screw shaft. I ground a small flat on mine to bed the itty bitty set screw into and it made a world of difference. Did it to all the ball screws after it proved out on my Z.
If that isn't it, check the tightness of the gibs. Also if your running a single ballnut, there is backlash there and you need to travel past that on an up movement and come back down to solid engagement to the screw.
Just some things off the top of my head to check. Areas I've had issues before and overcame.