Z axis issues, prusa mendel i2

I recently got a mendel i2 and so far I enjoy it a lot. Its a huge upgrade from my printr bot simple

How ever sense I have set my Z calibration to 1280 steps per minute (I used the calculator to determine the number) My prints start off perfect, as as you can see from the pictures but then towards the top last 2 layers of the 5mm calibration test it gets all messed up. Also the bottom step is slightly smaller then the rest of my steps, I measured it as 4.36mm when it is supposed to be closer to 5mm. I also have a issue with the Z axis that one side will some times get stuck due to the other side not moving at same time or being slightly off I'm not sure. If some one could help I would be VERY thankful. I'm not used to have 2 Z axis motors.

The first picture looks like it's caused by a lack of cooling. On smaller layers, the head lingers for too long in one spot and the layer doesn't have enough time to cool properly before the next layer is laid down, resulting in a melted look. Printing two at once will give the smaller layers enough time to cool.

Regarding the bottom step, it may be (at least partially) caused by the first layer being smooshed slightly into the bed and therefore not as tall as subsequent layers. This is necessary for good adhesion to the bed.

Regarding missing steps on one of the Z axis motors, make sure your vref for the stepper driver is set correctly. You could try upping it slightly and testing the Z axis travel to make sure it's smooth and doesn't miss steps.

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