It could be interesting to check if other GTK applications suffer from the same issue (Gimp, Pidgin, etc.).
Also, I guess it's a silly question, but as you can choose a different keyboard layout/input method per window, did you double check the Geany window is not using something else than English for some reason?

Last silly idea, what about the font? Can you open existing files and they display correctly, or do they display as katakana?

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