Burny, I agree that sometimes the best thing to do is start over, but I think that's when there is no hope left for the plants. Yes, I have been messing with the plants for 2 weeks now, but they have grown quite a bit. Maybe not as much as if they had never got the brown algae, but I have witnessed significant growth. I noticed the growth was slowing down when the brown algae started back up.
Had I just started over, assuming I had seeds to do so, I would have noticed the same thing happening eventually. But with help from everyone on this site, I believe I have pinpointed the problem. Light leaks from the lids by the net pots.
I have since cleaned out both totes, rinsed the roots off, and put new water in the rez. I also made the lids completely light proof (I believe it's completely light proof now).
As always, I'll keep everyone updated!