zelda-skyward-sword
When I entered the actual volcano in Eldin Volcano and dove off the metal platform, I landed on a tall rock platform witha Goddess Cube on it. I hit it witha Skyward Strike and it shot into the sky, but when I returned to the sky to open the Goddess Chest, I saw no indication of where it was on my map!
What gives? I've struck at least a half dizen other Goddess Cubes and they all showed up on my map in the Sky. Where's my treasure!?
Each cube responds to a specific chest. This guide outlines where the cubes are, and the location of their corresponding chest.
Those chests are scattered all over the world above the clouds, and can only be opened by activating the corresponding Goddess Cube in the the world below the clouds with your Skyward Strike. Once you do that the chest changes colour and can be opened. When a chest has been activated by a cube, it will show up on your map as a rectangular shape .
This is a Goddess Cube:
Here is a map containing the location of two activated chests (indicated by the rectangular blue symbol):
Here is a picture of an activated chest, which is now able to be opened:
(images taken from: http://www.ign.com/wikis/the-legend-of-zelda-skyward-sword/Goddess_Cubes)
Best Answer
You probably can't see it at the point of the game you're at. Spoiler alert:
Either that, or perhaps it's in Skyloft. Check your map once you land inside Skyloft.