On the pen, have you tried replacing the battery? Though I haven't had any problems with my pen, I do have a wireless keyboard/mouse which when the batteries are low starts sending multiple keystrokes even though I only push the key once, etc...
For the heat, only thing I can think of is that the apps are CPU/GPU intensive, and since it is on battery the tablet is trying to conserve power by holding off on the fan as long as possible. I haven't had any problems with this, though, so I'm not sure. You might also try change your PowerMizer (right-click desktop, its in the drop down menu there) setting to Maximum Battery so the GeForce2 doesn't heat things up as bad when running graphics programs.




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