When you said these "algea" apear only when lights on, it sounds like cyano bacteria or "red slime algea". I think you are right on when you say it cause by the stirred sand bed. When sand bed stirred, it will start releasing unwaned waste that was trap under your LR or deep under the sandbed. You tank might under go mini cycle as well. I would just siphon it out from the sand bed as much as you could. I wouldn't do too much water change at this time as new water into the tank is "more food" for those bacteria. Make sure you also limiting the light and food into the tank.
Oh when you try to siphon the sand bed, try not to go too deep which will cause more waste come out.
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