I have an image with a small skew, so I have rotate my image and calculated the correct x- axis scale in order to remove it.
When the scale is set to 1 (or a number bigger than 1.01 or smaller than 0.9999) the base point is in the correct position.

When I set the scale to 1.001, my base point moves! (the base point is on the cross-hairs, shown with a blue dot)