>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.

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https://bugs.launchpad.net/bugs/850427

Title:
  Boundary of screen no matching physical screen edge

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