You have to step on the large circles. Those are the only ones that teleport you to the right location. But, only step on the largets circles when they are bright green.
I'm actually having this same problem... I've been stuck since last night. I can't tell if that was a joke or not Darky (because of the wink), but I did put it there. The arrows did stop, but none of the circles turned green. Nothing at all changed that I know of and I still can't get the other crystals. How do you make them green?
Put the first crystal on the upper-right beacon, then use the newly bright green beacon to go get another one, then use it on the upper-left beacon, go get a third, and use it on the lower-right beacon.