I have seen this to on my Thinkpad X61 Tablet with 965GM, too. I think
the reason for the 42px offset is that the mouse cursor is a 42px by 42
px image which is mostly transparent except for the arrow in the upper
left corner. When the screen is rotated, the mouse cursor image is not
rotated, but the "active pixel" is moved to what is now the upper left
corner of it (which only contains transparent pixels).
I think I wanted to document it and took a screenshot using the gnome
screenshot utility. It not only didn't show on the screenshot, taking
the screenshot also fixed the problem (temporarily) and I forgot to
report it.
** Changed in: xserver-xorg-video-intel (Ubuntu)
Status: Incomplete => Confirmed
** Tags added: gm45 karmic mouse xrandr
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Mouse offset 42px and 90° when in rotated display
https://bugs.launchpad.net/bugs/432963
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