I am the person you quoted from the github discussion. I have recently been experimenting with this pipeline, ( ie Blender bone animations into threejs,) and have found that it is very very difficulty to find a reliable process that will work every time.
On my blog, I have compiled a list of 'tips' that allowed me to achieve success on some occasions:
http://dev.mothteeth.com/2012/10/threejs-blender-exporting-skeletal-animations/
To summarise, the most important things I found were:
Delete the Armature Modifier before exporting, or the animation will be all messed up.
Check that your Vertex Groups are properly assigned to the bones. ( In Blender, you can use automatic bone weights. )
Key all bones in the first and last frames of your animation. ( As you discovered, if you only have keys for the bones you have changed, ThreeJS won't infer anything about the other ones, and things will be broken. )
Even following these guidelines, I can't get things to work consistently, and have been considering using morph targets until the library matures a bit more. The file sizes for morph targets are much larger but they seem to be a more reliable option at this point, in my experience.
