sounds like it's not enough flow thru the fuge. the idea is: the greenies get first shot at eating the wasties and nitrates. so a full flow thru is best. you just have to figure out how to configure it in your space, and keep the flow from being too fast in the fuge itself/ although good mixing increases the absorbtion. then you let the water move to the skimmer compartment to complete the job before the water returns to the tank.
if you are using a 100 g rubber maid as the fuge, you will need a lot more light. like a MH or a couple 65 Watt PCs. you need enough light to make it like a planted aquarium to grow the macro. perhaps with a DSB in the tub and some rock for themacro to grow on suspended above the sand on eggcrate. thatwill leave the sand fully exposed to the water column.