What type of skimmer do you have? You can't go bare bottom without bad A* nutrient export in a FOWLR, or large consistent water changes. The algae is a plant, it is getting nutrients from somewhere. Can you get a pic of the general rock work? You could have overly porous rock with not enough flow to keep detritus and waste from settling on it. You could also be over feeding which is the main cause of nutrient woes.