Comment 2 for bug 850427

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Chris Halse Rogers (raof) wrote : Re: Boundary of screen no matching physical screen edge

From your Xrandr info:
"""

DVI-I-2 connected 1280x1024+0+56 (0xa4) normal (normal left inverted right x axis y axis) 376mm x 301mm

"""

The 1280x1024 bit is the resolution it's using, and the +0+56 is the position the X server has been told to put it - which means the X server thinks its 56 pixels down from the top. That's where your mouse is ending up.

This doesn't appear to be a driver bug. Rather, it's a configuration issue. Try re-aligning the monitors in gnome-display-preferences - the snapping zone isn't very big, so it's quite easy to set up your displays not quite aligned like here.