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It could be a mix of frag trauma and adjustment time. Corals often need some time to acclimate to new conditions, and they might not show their full potential right away. Also, the cutting might have come from a part of the colony with shorter polyps, so it could be a genetic thing too.

Glass carboys work great but are heavy. A two-gallon jug could be a good upgrade, and a magnetic stirrer might help if it can handle the weight. Consider a kalk reactor if you want something more hands-off.