Brian,
Being in NY, maybe you can take a live sample of your "m-algae" to a bio lab for identification/classification. FC levels of 40+ should be knocking out this stuff if administered for extended periods.
The only thing that jumps out at me is you stated you've been dealing w this for 9 yrs. Not a biologist, but most organisms can mutate and develop a resistance to medical treatments...as stated, if you keep your FC levels at MA kill levels until an OCLT = .5 or less, you should have it done. I would also run it a bit longer, let drift down and run a bit longer again. This is what I did for my MA kill.
Finally, from your pics, you have small dark spots and then shaded free from areas a bit darker than the liner. Can you define each? Thanks