I'm not really sure why that would be happening - although you have to select to use the Listing frame with navigation in a separate section, there aren't any separate colour options and the store theme/colours are all done in one place.

I suspect it might be something to do with the template you're using for listings, there may be some HTML in there that is affecting the colour of the navigation bar (the only way to know for sure would be to create a listing without using the template and seeing if the navigation bar is a different colour).

If that's not it, I have no idea, I'm afraid (and if it is it, I still can't be of much help as I would have no idea how to isolate and/or change the HTML causing it).