I wonder if there is not enough fertilizer in there? What is the analysis of the root tablets, and which of the Flourish products are you using?
Nitrogens low to none make it sound like the plants are gobbling all they can, and may need more, which hints that there may be other deficiencies, too.
Can you post a picture of the Sword with brown spots? I can think of 2 things:
Diatoms, also called brown algae, can grow on the leaf, hiding that spot from the light and leading to it rotting there.
Potassium deficiency; aquatic plants often show this with holes in the leaves.
Black fuzzy algae (Black Brush Algae, BBA) can grow in high water flow areas, and I have seen it in many spots in my tanks, too. It can be killed by treating with hydrogen peroxide, but try Excel, since you are already using it. When you are ready to do your regular dosing turn off the water flow. Then squirt the Excel directly into the algae. Leave the filter off for 15 minutes or longer (it will not harm the beneficial bacteria to be off a short time like this). Treat daily. Yes, I know you are only dosing every other day, go ahead and dose daily and treat the algae with that dose. If the black algae turns red, it is dead.