to me it looks like you don't have all that much live rock in your system...how many pounds do you have in it....I know this varies greatly depending on porosity of the rock but if you don't have enough in your system you will not have enough bacteria to break down organics. Over time couldn't this leed to huge algae issues as well
chime in more learned members cause i am a newb and could be full of crap. 
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Biocube 29 est 05/05/08, Koralia 1, 30lbs live rock, ,yellow tail blue damsel, pair cinnamon clowns, baby snowflake eel,Toadstool , metallic green mushroom, assorted zoos , kenya treen
180gall display, 190 pds live rock, virgate rabbitfish,bluejaw trigger, bubblletip anemone,yellow tang, sailfin tang,melanarus wrasse, cloud wrasse,
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