Got it. I understand now. Your cursor and pen don't overlap. You can't calibrate the pen because the cross hairs are our of range of the censor. Here is a trick I got from http://forum.tabletpcreview.com/ep121-slate/43622-pen-calibration-trick.html
1. uninstall your drivers, and restart your tablet (after you uninstall it, the pen wont work, so either have a mouse plugged in or use your fingers).
2. go to control panel, open tablet PC settings. Reset all the calibration data (touch and pen). When all the data has been reset, the reset button will be misted.
3. open command prompt (click start and type cmd in the search box).
4. type in, (or copy and paste, however to paste in command prompt you need to click the little black box icon in the top left corner, then select edit, then paste). Type in (make sure its all on 1 line):
tabcal lincal novalidate XGridPts=5,15,30,50,70,90,120,259,513,767,1021,118 0,1210,1240,1275 YGridPts=5,15,50,100,163,223,321,479,640,740,780,7 95
Then hit enter, it brings up the calibration screen but with heaps of points for you to touch. Make sure your pen is the first thing that touches the screen, then it will calibrate for the pen. After you hit the first crosshair with the pen, then you can rest your palm on the screen and do the rest. Just don't rest your palm on the screen until you touch the first crosshair, otherwise it will calibrate it for touch.
Give it a go and see if that helps. Remember you can set the cross hairs where ever you want with that command.