I found that whatever you have the least of (softies/LPS/SPS) will be most affected by the major population. I had a couple of softies in my tank when I was starting to really get into SPS. Both were doing poorly and were relocated to another tank. After that, the softies did fine and the SPS did much better. I found even running carbon that I had problems. However, this was before I discovered the brilliance of running carbon in a reactor.
I would try Myka's suggestion of smaller amounts of carbon changed more often. Overuse of carbon in large amounts can cause problems for SPS as well.
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