Check the settings in the thumbnail on the left to see if it says Engrave. Those do look like they are set up correctly, were they created in Illustrator?
When you save your SVG files, make sure you are doing it according to the suggested settings in the tutorial below, and Glowforge currently prefers that you use Save As instead of exporting the SVG. (Fewer interpretation problems.)
If this doesn’t resolve the problem, you’ll want to start a new topic for the black filled shapes so that support can address it. Your original missing artwork issue was resolved I believe, and they don’t read all the posts for additional issues that folks might add to threads. 