I doubt this is causing your problem but I thought I'd mention it anyways. I've read that lava rock is a poor choice for saltwater aquarium rock because it will leach undesirable metals like iron into your water. If I could remember where I read this I'd post a link for you but unfortunately I've forgotten.
Based on the other information you've provided all I can think of is to keep doing water changes, perhaps get a better skimmer (I don't like coralife anything) and give us some more information. For instance, how old is your system? What are your other water chemistry parameters? Do your tanks contain any livestock yet?
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