If I am picturing things correctly, I believe you are fine for this point in the calibration. Only use the disc color as feedback during calibration: yellow means a capture will not work, while a green disc means the Kinect has a good reading to use for calibration. Ignore the position of the projected disk until after you have captured at least nine tie points, then the projected disc should closely follow the real disc.
Oliver covers this in his calibration video, but I know I was confused the first time I saw the disc projected on the wrong side of our sandbox.
@robbo I agree that turning the camera or projector is a solution. Calibrating the Kinect and projector as they are should also work.
I was wrong (darn faulty memory) to say the virtual disc will project onto the real disc after calibration, but the red cross-hairs will follow the center of the real disc. And the sandbox projection should match up with the sand forms.