I have a machine (Fujitsu T5010 dual digitiser) where the touchscreen and pen calibration is out. On the top left corner it is correct; on the bottom right it's out by about 2cm in both axes. Running the calibration program from the control panel doesn't fix this; in fact touches near the right and bottom edges don't register to the calibration program - the touch 'bubbles' appear on the far right/bottom edges of the screen - i.e. the screen is registering the touch, but the calibration programs seems to think they're too far across to make sense, so it ignores them.
I've tried un-installing and re-installing the touchscreen drivers, to no avail.