I have just setup the Ultimaker today and the Y-Axis motor does not seem to be working correctly. The X-Axis moves smoothly, but the Y is extremely jerky and erratic.
If I manually move the head with the "Move Axis" function, I can see the motor jumping back and forth, even if I am moving it in only one direction. I removed the motor from the unit to see if there was any friction etc. causing the issue, but the same problem occurs.
The Motor appears to move randomly, and not in a smooth continuous direction as the other motors do.
Now, the strange thing is, if I plug the X-Axis motor into the Y-Axis port, it will work only in one direction. Also, I am able to get the head to "return to home", although it does it in this erratic motion on the Y-Axis, juddering back and forth "violently". The wiring appears correct in the motor and plug that connects to the board.
I just connected to Cura, and it upgraded to version 13.03, from March 1, 2013.
Thank you for any help you can provide.