I encountered the same problem. You can get around it by setting the
window that you want to use to "always on top".
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https://bugs.launchpad.net/bugs/1037864
Title:
Sikuli does not work
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Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/1037864
Title:
Sikuli does not work with Ubuntu unity 2d
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https://bugs.launchpad.net/ubuntu/+source/sikuli/
