I copied console.py in my home config dir (~/.config/geany/geanypy/plugins) and forgot to rename it (but file content and plugin name was changed). After that I had doubled plugin set in Python Plugin Manager:)
In short if you have two plugins with same file name in /usr and in ~/.config you will get this bug.
Build date: Apr 15 2014
-- Best regards, Pavel Roschin aka RPG