A little difficult to tell from the images you posted, but looks like you have duplicate shapes, sitting on top of each other, which will cancel the fill. Fills use shape boundaries to define and toggle the fills for the shapes on that layer. You have things on several layers, which will change the way fills are calculated.
Additionally, LightBurn uses wireframe for shapes, and does not use Stroke or Fills set from an external editor.
This post should help with understanding how LightBurn chooses what to fill and when.