I have reached Eldin Volcano and am trying to activate the Goddess Cube at the end of the forked path. No matter how many times I hit it, it won't flash. I have followed the guide, so don't think I have missed anything. I didn't do the Pumpkin Juice side quest. Could that be why it isn't working?
Hold your Wiimote (sword) up and let it charge a Skyward Strike, then slash it so the sword beam hits the Goddess Cube. This ALWAYS works on Goddess Cubes, there's no reason why it shouldn't. The corresponding chests may not be obtainable right away (in the sky), but there's no bugs about these things so it should work perfectly fine if you hit it with a proper Skyward Strike.