Hi guys,
I've had this problem with my reprap, and it had to do with Z axis : it wasn't correctly carried, so Z axis pushed and pulled the extruder slightly, with the exact Z sscrew shape of the axis on the final model. It looks like the same problem here, you shoule check if the shape of your model matches the shape of your Z axis, and maybe you need to check your machine (i dont know the ultimaker design, so that's the best i can tell...)