I have a Duoclear system (one half of the unit is a SWCG, the other half is a Nature 2 cartridge). I was keeping the chlorine level around 1 per the instructions, but was suffering from brownish stains appearing on my pump and filter baskets and my return eyeballs. Last fall I yanked out the Nature 2 part, did an ascorbic acid treatment and removed the stains. So far (including the tail end of last season - maybe a couple of months) and almost three months this year, I have not had the stains return.

My suggestion - get rid of the Nature2 system (you don't have to do any plumbing, just pull the cartridge out and don't replace it) and run your chlorine at the recommended level relative to your CYA level.