Black / brown stains on pool bottom - help

All of a sudden I am having issues with black / brown stains on the bottom of my pool. It is an in ground Marcite pool with a salt chlorinator. At first they mostly seemed black and I could scrub them off the bottom. Now they are mostly dark brown and rather than being little circles of 1/4 to 3/8 inch they look like they have tails like a comet.

The water is balanced just fine and I have shocked the pool twice with no luck. What can I do to get rid of these?

Thanks