diatom & lightng ?'s

The pictures do indeed indicate cyanobacteria. If it seems to be occurring in areas with lower flow, then detritus settling could be acting as a substrate-source of nutrients for them to grow. Try manually removing the patches and then increasing flow to see if that helps.
Thanks again Amphiprion, I will work on this. I was just a little worried about the anemone wanting to get up and move, he has just recently came out from behind the rocks. I have tried to work the lr in a way that gives me water movement, is it possible that maybe I have too much rock?
 
That is also a possibility. I tend to err on the side of slightly less rock than most, though. Good, open structures are optimal for this.
 
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