Try applying the patch at
http://sourceforge.net/tracker/?func=detail&aid=2829716&group_id=163434&atid=827735
to the source code. (It adds a workaround for this annoying bug in ubuntu's 
GTK+ and Synaptics device drivers).
Hope this helps.

Denis

** Bug watch added: SourceForge.net Tracker #2829716
   http://sourceforge.net/support/tracker.php?aid=2829716

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Xournal does not work well with touchpads
https://bugs.launchpad.net/bugs/348706
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