Yeah, it is not a calibration problem. In Other applications the pointer is spot on, but in Dosbox it is off by a random amount of pixels, depending if it is in full screen or not.
In the 'windowed' mode, the pixel is off by maybe ~20 pixels or so, constantly. In full screen mode, it is off by a variable amount that seems to be dependent on whether you clicked on the outside of the virtual screen rectangle or not.