I am using the sigil on the boulders which sink into the ground, but they don't go all the way down into the ground and I can't get to the chest. Anyone else have this problem? Is there any other way of getting the 3rd crystal without having to go through the rocks?

Have you tried going in from the water side of the boulders? If you go up to the big bridge (where you put the 3 pieces in), you can jump off the bridge and swim down (fighting the current) into the other side of the boulder cave. From there, you can jump back into the water and continue out to the double waterfall area. That's what I did Just avoided the boulders all together!