First on the plant itself...carpet plants are not always easy to grow because they usually need strong lighting, and with that comes more nutrients in balance. Some sites (Tropica for one) suggest this plant, Micranthemum tweediei 'Monte Carlo,' requires good light conditions and CO2 diffusion.
As for CO2, you are wise to discontinue the API CO2 Booster. This is glutaraldehyde and water, and this disinfectant can melt some plants outright. The fact that it is sometimes suggested to kill brush algae sounds warning bells, as any toxin that will kill algae is dangerous to say the least. If it should be overdosed, it can kill plants, fish and bacteria. It is used in hospitals to disinfect surgical instruments and kill bacteria elsewhere such as in embalming fluid. Don't let any get on your skin, as others have reported skin burns.
To get the light sufficient for the plant, it might mean algae has an advantage. We would need to know the light data to offer much on this. If the brown is diatoms that is one thing that may clear up. There are some fish that will eat diatoms, but I am always leery of suggesting fish because I have no idea if they will work or not in this particular tank.
Flourite by the way has been shown to have very little if indeed any benefit for plants, I had it for two years and then tossed it out, and others have said similar. I still had to use plant additives the same as with inert sand or fine gravel substrates. Flourite is also dangerous for substrate fish (cories, loaches, etc).
