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Maybe some organic left overs from a previous life is just changing color faster than the rock now it is back in the water. How did you clean the rock before putting it back in the tank.
Vermitid snails have a small curled shell that is permanently attached to rock or glass. Did you seed the tank with anything? I started my tank with dry everything ( acid washed) but seeded for pods, with that came barnacles and sponge.
What about frags, have you added coral at all? Rock left to dry for 3 years should be void of all life. I don't know if eggs or spores can survive that. Maybe someone with that specific knowledge can weigh in.
They may not be alive, but you can clearly see the Vermetid snail shells in the picture IMO. Just as an example, on the far left about the middle of the picture you can see a shell with a twist. Now that you know what your looking for, there all over the rock.