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.
If this is the Goddess Cube across the lava river (in the room one or two before the dragon), then you can't reach it until you get the True Master Sword. Until you get the True Master Sword, your Skyward Strike is not powerful enough to make it across the lava river.
If you are playing in Hero Mode, you can get the Goddess Cube right away because your Skyward Strike is already at full power.