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What are the layer modes of each layer? Your top layer could be in something else than Normal mode. For instance if your top layer is in "Difference" mode, over transparency the result is the layer itself, over another layer it is sometihing else.
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Using Gimp 2.10.18:
Strange, seems to be a function of the zoom value here. The effect shows at 50% and smaller but not higher values.
Must be a function of the screen rendering
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Yes, now I noticed that also. Rich, thank you for the explanation.