Stains on Vinyl

Hi,
I'm a new home owner that inherited a 33,000 gal inground pool. I took the cover off for the first time in early May and discovered a green mess which I've cleaned up nicely. The numbers are great FC=6, CC=0, pH=7.5, TA=110, CH=130, CYA=50. The pool took a while to clear up and I discovered brown staining on the liner. The stains have straight lines so I don't think it's due to leaves. They run along the bottom as well as up the sides. I had the water tested for metals and it came back negative. There is a heater that's about 10 years old that the previous owner said he only used the first year. I currently have it bypassed. There is also a Nature 2 cartridge installed but hasn't been replaced so it is at least 1 year old. Does anyone have an idea on how to determine the cause and the best way to remove them? I've attached a photo hoping you can make out the stains. Thanks for any assistance you can provide!
http://photos.wollerfamily.com/photo...-Fd3Kt26-M.jpg