Wow, those are some great first projects!
I have some ideas about why you are having trouble with the flower. Although you uploaded a PNG to this forum, it appears that you sent an SVG of the Inkscape file to the Glowforge. To me it looks like you sent a file where the flowers (as well as the vine leaves) were specified with a stroke and no fill. But because they are closed figures in the GFUI you can choose to do them as engraves and fill them in. That worked fine for the leaves, but the flower is a little more complex and you were at the mercy of how the stroke direction closed the figures. If you actually want the insides engraved, you need to change the parts you want engraved to fill, no stroke. That may require you to separate parts in your Inkscape file so some are stroked, some are filled. This may be more work that is worth it to you. You can learn more about this type of thing by looking over the tutorials in Glowforge Tips and Tricks. I would look for Inkscape tutorials in the 2D Vector Design section.