just a guess... it could possible be from where it had coralline algae growing on it, and then the coralline died. are they actually pits, or just marks?
Calcium: 380
Mag: 1300
kH: 10
I have always had troubles getting Calcium above 400. I have a calcium reactor but before that I have used Turbo Calcium. After dosing Turbo Calcium the levels still never got above 400.
what's your pH at? (might be why you can't raise it) and what do you use for buffering calcium?
its an expensive test, but you could always test iodine as well. it could just be your emerald is a tad different.