I've run into this issue several times in Painter and photoshop. Never really figured out why nor have I found a solution (or at least a reason) when searching.
The issue is that at times when I lay a stroke of dark color over another color that's darker about a tone or so, the stroke above won't get painted. Now, if I use an lighter color or a brighter color (less neutral) there is no problem, the color below is covered by my new stroke.
This usually happens with the more subdued, dark and neutralised colors.
Any way to 'fix' this, or at least is there a reason and logic behind this so I can understand the nature of it and work around it and know when to suspect it might happen.