"...After an upgrade to Ubuntu 9.10 (Karmic Koala) I noticed a few random issues in Eclipse has popped up. Most notably, I was no longer able to click the OK buttons on pop up windows – I had to highlight them with the mouse then hit either space or enter on the keyboard to select them..."
Summary:
If you encounter such GDK problem, you may set the environment variable BEFORE running your application:
export GDK_NATIVE_WINDOWS=true
OR
export GDK_NATIVE_WINDOWS=1
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