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Er.
Looks like it could be a problem related to opacity: lighter strokes come through as more transparent, which on a white background would render them brighter. It might be worth checking the tool you're using, to see if it's set to translate stroke weight to transparency instead of thickness.
This is all, of course, a wild guess.
For some reason, on a brand new blank canvas in Paint Tool Sai, I'm getting random colors. The color changes on the canvas even though I'm only using one color.. I don't know how to explain with words, so here's a picture.
[link]
Does anyone know why this is happening? D: