It would be good to get a cya measurement. I am wondering why you would have gotten stain with a low chlorine level - did you shock when you opened the pool? Or maybe they happened when you closed with high chlorine. High chlorine along with high ph will let the metals precipitate out of the water and stain the surface of the pool. Since you have already tried just the sequestering agent and did not seen a lightening of the stain, you may have to use the regular stain treatement with ascorbic acid - usually if the stain is old it is more stubborn and needs the ascorbic acid. Here are some links you can use to buy it:
http://www.chemistrystore.com/Ascorbic_Acid.htm
or

http://www.msm-msm.com/store/agora.c...scorbic%20Acid

Here are the directions:
Take your chlorine down to 0, if there is chlorine in the water it won't hurt, it will just eat up the ascorbic acid, so you will need more to get rid of the stains.
You will need about a half to one pound of ascorbic acid per 10,000 gal. I like to go lighter on it and see if all the

Put the filter on circulate.
Use a cup and go around the perimeter of the pool and drop it down the sides as you go.
Let the ascorbic acid circulate for 1/2 hour. You will be amazed how the stain just disappears before your eyes.

If the stain is not all gone, leave the filter in circulate and add more ascorbic acid close to where you still see stain. Leave it in circulate until all of the stain is gone. (add more ascorbic acid if it circulates for 1/2 hour and there is still stain)

When the stain is gone, add enough sequestering agent for the volume of your pool - more is better than not enough.

Put the filter back on filter and leave it on 24/7.

The ascorbic acid will bring your ph down, after 24 hours you can start to bring up your ph and alkalinity - use baking soda first, it will raise both ph and alk. Make sure you test in between, because you don't wantyour ph to go any higher than 7.2. If your alkalinity is in range, and you still need to raise your ph, use Borax to take it up to no higher than 7.2. After 48 hours you can start to bring up your chlorine. You want to do this slowly. It will take a lot of chlorine - I prefer to use bleach only at this time, and try to take it up to your minimum chlorine for your cya according to the "best guess chart" Do not shock! Do not shock for at least 2 weeks! Make sure you keep your ph low for (7.2) for a week or two - it won't be hard because the ascorbic acid will help it stay low. Once your chlorine starts to hold, it means that you have used up the ascorbic acid in the water and it will be easy to rebalance the pool back to your regular parameters. You may want to use a polyquat algacide as a deterrant to getting algae while your chlorine is low.
Let me know if you have any questions.