I find that of all the four rotation orientations: primary landscape is the only one where the subpixel will work properly. If it's rotated into primary portrait or secondary portrait or secondary landscape, then stylus clicks just won't go where you want them to.
You can try bringing up the virtual keyboard and hit Esc to get out of the config window, or plug in a mouse and regain control, or just rotate the screen back to primary landscape. The only problem is that on motion computing computers, and on some other tabletPCs, the buttons wind up on the right-side of the screen -- which is a little more difficult if you like having them on the left side, for handling flipping functions, etc.
(Win7x64, TVP Pro 9.5 32-bit)