Your water permameters are fine so I don't think it would be that. I have a mixed reef loaded with sps and LPS. I have my sps up top and LPS on the bottom. I have my flow cranked at 100% and I never have any issues. However I have noticed that without wrasses in my tank for a few months the amphipods will get out of hand and eventually mow all my LPS. And for those non believers I have pics. They ate my acans, ricordias, zoas, and even some chalices. They only come out at night making it very hard to see. If I were you I'd go look at your tank a few hours after your lights go out. It's possible you could be having the same issue. If you have wrasses or other predator fish though then it could be something else.
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