Sounds awful, Matt
I'll bet a lot of detritus is being trapped in the GHA. Try turkey basting it a couple of times a day to see how much gets into the water column. Hopefully your skimmer will remove it.
Also, you running a sandbed or BB? If a sandbed, when was the last time it was changed? Could be loads of nutrients in the sandbed. If running BB, are you able to get all the detritus out from under the rockwork to siphon it out? Most of the detritus in our BB settles under the back rocks under the powerheads. We use a turkey baster to blow it out to the back of the tank for siphoning.