You did not mention if you are using carbon or not. If not it should help with most of the nasties the skimmer is missing,.. also I (over)feed my fish to help feed my sps reef as well as daily broadcast feeding with zooplankton. it sounds like your tank is starving. dont be afraid to feed the tank, it appears that you are keeping up with testing so you are able to control your nutrient params. I run 8 oz gac in a cannister and 8oz passively in bags in the sump (replaced monthly) feed the tank, run carbon, change 15% water/week ,test