I experience the same problem, bug reported in:
https://bugs.launchpad.net/ubuntu/+source/xorg-server/+bug/1085031
everything detailed in this url.
** Changed in: xorg-server (Ubuntu)
Status: Expired => New
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https://bugs.launchpad.net/bugs/767315
Title:
xinput 2 "Coordinate Transformation Matrix" not affecting all events
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