Welcome to Inkscape Community!
First, thank you for providing such a thorough presentation of the problem! It looks like you have applied a path effect (LPE) to the path, called Power Stroke. That changes how fill/stroke behaves. If you zoom in, you may be able to see that the stroke really isn't like a regular stroke anymore. It now has a yellow fill inside the stroke, and a black border, which yes, is also called a stroke. I know it's confusing.
If you switch to the Node tool

you'll see 2 kinds of nodes - gray ones (the ones you set) and some new pink ones. If you grab a pink one and drag it, you'll see that the "power stroke" can be made wider (or narrower). If you make it wider, you'll be able to see the yellow fill much easier.
Did you have some reason for applying the power stroke path effect? I don't think it's possible to apply it without realizing it....well I guess it is possible, if you're like I was as a newbie -- just clicking things to see what they do. You may have applied the power stroke and thought it didn't do anything, and moved on. But if you are trying to achieve some particular effect, let us know, and we'll be glad to try to help.
Just for future reference, here's a little article/tutorial I wrote, to help people with this kind of problem:
http://forum.inkscapecommunity.com/index.php?action=articles;sa=view;article=18. At the moment, it doesn't cover this issue, so I'll plan on editing it asap, to include this problem.