Christy, are they on all of your rocks, or just a select few? One possibility, and I know you wont like it, is to remove each rock 1 by one and kill it off or scrub the living bejesus out of it then put it back. You could do like 1 per week or something and it shouldnt upset your tank too much. Yes you will have to unmount some frags but I'll take any of the broken bits
How is the skimmer now, settled down?