I have just recently run into an issue where when I use the pen tool to draw a shape the shape will only show the stroke, but not the fill. The shape has both a fill and stroke color set and both the object and layer are set at 100% opacity. I'm not having this issue when I use any of the shape tools, so I assume it must be just an issue with the pen tool.

I first encountered this problem on an older version of Inkscape, but I updated to the latest version and I'm still having this issue. 

Before proceeding further, I'd reset the preferences. https://inkscape.org/forums/questions/getting-back-to-square-one-and-starting-over-its-easy/

I've just reset the preferences and restarted Inkscape, however I'm still encountering this issue. I feel I should note that when opening the file I was working on in other programs, it still displays with a stroke, but not a fill.

I've had that trouble too. If I recall correctly, and I may be wrong, but I think I swapped the fill/stroke at the bottom left of the screen and then it suddenly worked. It's happened a couple of times.

A double-click on the pen tool will open its settings dialog. It may be set for a specific style.

I double clicked on the pen tool and both the stroke and fill were unset. Oddly now when I use the pen tool, the fill shows, but only on new shapes, not the original one.

On the right is the new shape I drew, on the left is the original one

The status bar indicates that the path has a power-stroke effect applied.  That may be the issue.

Sure enough, that solved the issue. Thank you so much!