I believe that before this forum lost all of its messages that a post was made that stated shocking it at very high levels with liquid chlorine and keeping it at that high sustained level for 48 to 72 hours would go a long way to removing these stains. They are caused by the tannin in leaves and the chlorine helps to dissolve the tannin.

I have done the same and it did help, although some minor stains do still remain. They are slowly (three months) going away as I keep it on the higher end of Ben's CYA calculator for the normal chlorination measure. I have many leaves falling into my pool.

Hope this helps.

Good Luck