Okay before anyone wastes their time replying I just review the other post regarding this (http://www.polargraph.co.uk/forum/?mingleforumaction=viewtopic&t=122), Im in the process of trying that.

Hey up Chris, if the "c" key doesn't bring up the console then you might benefit from an updated version of the controller.

When this happens to me, it's because of some bad value I've put in for mmPerRev or stepsPerRev - or rather, it's because those values have led to the internal values for stepsPerMm and mmPerStep being miscalculated. In the older versions of the code it was more important to upload these values in a particular order, and then reset, and do a magic dance and say an incantation, but it's better now. I believe.

The why:
The first move works because it doesn't need to do any calculations - the controller just says "set the left motor to 1234 steps, set the right motor to 5678 steps". It's easy, and the machine doesn't need to know the size of itself, the size of the sprockets, the size of the steps or anything.

The second move doesn't work because now it's attempting to convert the input coordinates into a different coordinates system, and for that to work it needs to know all the things above (size of sprocket, size of machine etc). It's converted them wrong, and resulted in a set of much lower numbers than it needs.

I would try updating to the newest versions of the firmware and the controller. Just the new controller on it's own might help, because there might be some message in the console that will illuminate something. It won't fix it though, I don't think.

good luck,
sn