Is there any chance you have a ladder or steps in there that could be hiding some algae? How about a light? We've had people chasing the FC loss for days and found it behind the light or inside the ladder pipes or beneath the steps.
I haven't put the ladder in there yet. We have built in steps on the shallow end as well. They look pretty clean. There is a light right under the diving board. I just realized that you can't really see it in the picture because of a shadow. I haven't looked inside the light yet, but the outside doesn't look bad.