I'm having an issue with a jerky Y axis during printing. The bed moves back and forth fine using manual controls, but during printing, it jerks with every step. In the picture, you can see the sawtooth pattern in the supports. What would cause this to occur?

IMG_6391 by David Bitton, on Flickr

Have you configured your steps per mm properly yet? Do you have microstepping enabled yet?

i had that problem and it was the tension of the Y axis belt, give it a look