I have a JFrame with a JLayeredPane. On the first layer there is a table, then above it there is black transparent layer that allows me options and what-not.

I animate the arrival of this transparent layer. However when I do this the panel seems to loose it's transparency, that is until I interact with the base layer, THEN I see through the transparent layer again.

Sometimes, when I start interacting with the textfield or button on the transparent level, it starts displaying pieces and bits of the lower layer on the Transparent layer.

Am I missing the need to repaint something or....I'm not even sure. Why is there this visual bug please?

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GlassPane/JViewport(with custom RepaintManager) or JLayer (just the painting illusion, not real Component)

So how do I make this stop. I'm not sure I understand your post.

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