Here's a simple test to see where the problem might be: rotate your screen.
I did it with mine (the one in many pieces on my desk) and to my surprise
the misalignment didn't occur at the physical bottom (Apple logo) of the
Newton, but at the screen bottom. Rotating the screen the other way caused
the lines to draw _above_ where the pen was. Seems like it's a software
deal with the alignment routine. Curious.
Now, I do have to admit that I was holding the whole thing sort of together
in my palm, and the LCD and touchscreen were a little loose relative to
each other, but the offset is still significant nonetheless. Next I'll have
to try repositioning the LCD after the alignment routine. What fun!
Give it a try (the rotating the screen part, not the disemboweling your
jc, who's got a few loose and/or missing screws.
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