Try to make a test cube that is abit higher than where your problem begins on your print.
I also had perfect test cubes 20x20mm and 40x40, but when I printed something higher I got problems on my Prusa I3 with lead screws.
I changed out the motor, cupling and rod with a fully integrated motor, and then may prints became much better.
All in all I got tired of fidling with the Prusa i3 and bought an Ultimaker 2. More prints and less adjusting and tweeking.