Why do lines appear faint when working with layers?

I'm drawing using a Cintiq and using layers. When the image is then flattened, the lines become much blacker. I don't want the line quality to look different when in layers than when flattened. When I work in Sketchbook Pro, it looks exactly the same in layers as when it is flattened or saved as a jpeg, so why does Photoshop behave this way? Is there a way to fix this in Photoshop? I'm hoping so because it's a real deal breaker for using Photoshop to draw.
Here is an attached sample to show the difference. Thanks.

Perhaps it because Photoshop is not displaying the transparency grid and you perceive your lines darker when displayed on a white background. That is the same thing that happens when you flatten a document. Empty and transparent pixels become 100% opaque because a background layer does not support transparency. If the canvas default color is white. White is added to all pixels till the pixels are 100% opaque. You may perceive the change in contrast as your lines becoming darker.
Here is a screen capture of your example with white remove. One copy with no background the other over a white background.

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Why do lines appear faint when working with layers?

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