hmm, inkscape seems to have a bug where its renderer prefers the "stroke=#color" attribute and renders that color, but the stroke paint panel only affects the style attribute and doesn't see the stroke attribute at all?!
I can't see in the code how it clears the attributes, but I have a memory of it doing so in the past. Probably versions below 0.91. Can you report your bug to https://inkscape.org/report please?