I'm not sure, but that sounds like an issue with your graphics card. Have you tried going under Preferences > Performance and in the upper right corner, disabling GPU? Also, could you post a screenshot if possible so we have a visual of the issue that you're dealing with?
It's also possible you have set your brush blend mode away from Normal in the Options bar to one of the blend modes that can significantly darken the colors? They wouldn't be pure black, but depending on the color and blend mode, they could be very, very dark when one brush stroke overlaps another. Just trying to guess.