Medium brown spots

[Huskerdee]

We have a 32'x16'x52" pool with a DE filter. We use well water that Zi know has metals. I use the tedious method of shocking do the metal drops out of suspension do I can permanently remove them. I know this causes staining so I used Stain Away to remove stains. We also had some green algae upon pool opening this year. I used both Stain Away for removal of metal stains and Pool First Aid for organic stains. I vacuum and brush daily and check balance at least every other day, the balance is great and water is crystal clear. However we have several brown spots on the floor of the pool. I have tried brushing and vacuuming like crazy but they do not go away at all. They are like sand color brown and brushing and chemicals do nothing. The only thing I see it does is smudge them. Too cold to get in the water to do anything. When I brush it would be like syrup on a table. When you rub with your hand it just smears. Any ideas? I would greatly appreciate it. Thank you