if your ft water is flowing through the duckweed tank, you may have too much flow..
i ended up taking one of those small plastic yard ponds, and setting it next to my main system, i used the ft water to fill it and put the duckweed in it.. at first i had an airstone in the duckweed tank, as well as a couple minnows and a single crayfish..i also put the wife's pond lilly in it....after about a week i thought it wasn't really doing much, so i removed the airstone and put it back in the ft.. thats when the duckweed growth really took off..
it was in the shade most of the day, and got maybe 3 hours of direct light..
so my experience showed me that it really prefers "still" water.. i have compromised and put air in my tanks (via sponge filters) because of the livestock, but try to tune them fairly low..