In an earlier thread that I was helping with today, I wrote the following to somebody who was complaining that they constantly had sand all over their pool floor. I'm going to copy and paste my reply to them here. It doesn't totally apply to your situation, but part of it may since you aren't sure what the brown stuff is on the bottom of your pool.

Below is what I wrote in the other thread:

Is it possible that it is just dirt/dust?

My pool has a vinyl liner and underneath it is a foam pad that is taped together with tape. You can see these lines underneath my liner. I can vacuum my pool and have it look spotless but then hours later when the water quiets back down, the dirt/dust that is in suspension while I am vacuuming drops back down and always resettles in those 'lines.' No matter how slowly I move that vac head around and no matter how spotless it looks when I am finished with the vac, it reappears. This was also true in my previous liner pool. It is no big deal, though. Of course, I want my pool perfect but hey, there is dirt out there in the world and there is no way I'm going to keep it out of my pool. As soon as we get in to swim, that little bit of dirt gets swished around back into suspension again and you can't see it.



Now, Matt, what I want you to try: Turn your pump off for awhile (like maybe overnight tonight) and see if stuff settles on the floor. Then, turn the pump back on and very slowly vacuum the pool floor. Then, wait and see if that makes a big improvement. If it is dirt/dust and you are brushing the pool frequently, you are getting it all into suspension and that could be clouding up the water.

I'm not saying you didn't have algae; you obviously had something going on with CC readings and with overnight chlorine loss. But, I'm just wondering if part of it could actually just be dirt/dust. How long has it been since you vacuumed the pool?