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I'm not sure what the problem is though, so I'll ask a few questions.
When I select a stroke color, it appears to be normally selected.
Do you mean that you choose a stroke color before you start to draw? Or are you talking about selecting a stroke that's already been drawn?
But when I draw a stroke with the [Pencil tool], it does not appear until I hit fill where it then becomes a skinny oval.
What do you mean by "hit fill"? What becomes a skinny oval? Are you talking about the Pencil stroke? A stroke with rounded end caps could look like a skinny oval, if it's a straight line.
The fill also does not select properly. It gives me the 'area is not bounded' message even when I am 99% positive that the area is bounded and looks like this:
"Area is not bounded" message only appears when using the Paint Bucket tool. Is that what you mean by "hit fill", that you're trying to use the Paint Bucket tool to fill inside a path drawn with the Pencil tool? The screenshot you provided doesn't show your drawing. It shows the style only, of some unknown tool. Even if that's the style of the Pencil tool, it doesn't help me understand what the problem is.
Could you provide a screenshot of the drawing -- or better yet, of the entire Inkscape window with the drawing on the canvas?