Georg Klimm, I can see that after a long process you came to an old
conclusion, or well known fact: in the new Xorg server, the server
installs the mouse by default. Then, the mouse uses the xev
infrastructure which causes the swapping. It is still blurry to me how
it manages to get the penmount data and translate it. Nevertheless, the
idea is that it gets some input from the penmount device and translates
it into the mouse (relative) coordinates. As a result, clicking twice on
the screen on the same spot will bring you always on a different place
:)

What you can do is to remove the mouse_drv by moving the:
/usr/lib/xorg/modules/input/mouse_drv.so to some different file name.
This thread is about Ubuntu, but your Debian experience might shade some
light on the solution.

Let us know...

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no calibration tool
https://bugs.launchpad.net/bugs/227183
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