I can answer only part of the question. I know for a fact that PolyQuat (if that's the algaecide you used) is a very viscous polymer which means it disperses very slowly and I believe it is also denser than water (not positive on this last point). I know that it is recommended to keep the pump running quite a while after adding it so that it thoroughly mixes -- probably at least 8 hours.
What I don't know is if it's acidic. It does not appear to be, but I don't know for sure. If it were acidic and settled at the bottom of the pool, then that might explain it. You (or someone else with PolyQuat reading this) can always add some to filtered water and see what sort of pH comes up. Or take some pool water and add some PolyQuat to it in a small bucket and measure the pH change.
Sorry I couldn't be of more help.
Richard
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