Fist let me provide some basic information :
Pool - Above Ground - 24ft round - approx. 13,000 gals.
Frog inline Chlorination system (Mineral pack + Chlorine pack)
Filtration is Sand filter with 1 horse pump

I've had the pool now for about 7 seasons. The first liner (yes I said first liner), started developing brown staining after the first or second season and progressively got worse. I spoke with the pool company and there best guess was ground mold, which I was told once it takes root in the liner there is nothing I could do. So about 2 seasons ago I replaced the liner, and had them install a plastic matting under the liner to prevent this from happening again. Well I've now stated seeing this brown staining again. I asked the pool store if the Frogs mineral pack could be causing it and was told no.

A few additional pieces of information which may help is I have wedding cake steps in the pool. To hold them down the steps have 3 bladders which need to be filled, the instructions call for sand but I chose to use peat gravel (bought a couple of back at the home depot). I have test strips but to be honest haven't used them much. I have had the water tested at the pool store a couple of weeks ago and was told I needed Ph Up and Alkalinity UP which I added. Had the water tested again today, and was told my phosphorus was a little high so I'll be adding the appropriate chemical for that tomorrow. Here are the numbers provided by the pool store:

Free Chlorine: 0.0 ppm (I shock every weekend, and have 2lbs of shock waiting to go in but was told by the pool store not to shock it for 2 days after applying the Phosphorus chemicals
Total Chlorine: 0.2 ppm ( I also bought a new Frog backpack to replace the one that is almost empty, but again was told to wait on installing for 2 days).
Combined Chlorine: 0.2 ppm
PH: 7.5
Hardness: OVR247 ppm
Alkalinity: 35 ppm
Cyanuric Acid: 38 ppm
Copper: 0.1 ppm
Iron: 0.1 ppm

Sorry for the long post. I asked them if the staining could be Metals, but they tell me my metals are low. I guess I'm hoping someone will tell me its not ground mold, but something easily correctable so that I don't end up having to purchase a third liner with in the next couple of years.