The more I think about this the more I believe that it is indeed some form of algae. I do have a fair amount that clings to the walls and it is typically found in the low flow areas first.

I vacuumed yesterday evening and this morning brown deposits again could be found throughout the pool. Not a huge amount, but it has definately redeposited to some extent.

I am going to go ahead and shock as Matt has suggested and I will keep you posted with what I find out. As I said, I have had this issue for about a month, so if it clears with some heavy shocking then I can feel certain that it was indeed some form of algae.

Riles