This is fixable with a one-line change, and is resolved in 0.90.4.
See:
https://code.google.com/p/autokey/source/diff?spec=svn557&r=544&format=side&path=/trunk/src/lib/gtkui/notifier.py&old_path=/trunk/src/lib/gtkui/notifier.py&old=541
** Changed in: autokey (Ubuntu)
Status: Confirmed => Triaged
** Tags added: bitesize
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https://bugs.launchpad.net/bugs/1056799
Title:
autokey-gtk blocks keyboard input on second attempt to execute python
script in 12.10 quantal
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