Hi masspool,
It sounds to me like the stains are already there but yellowish--which combined with blue water will appear green. I don't know what to tell you to do, but am bumping this post up so that others may be able to help you.
How are you testing your water? I'm a little suspicious of your TA and CYA readings -- the only reliable test I know for CYA (the turbidity test) can't distinguish CYA levels less than 30 ppm.....and you report a drop in TA from 60 to 47 over a 12 hour period...

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