I noticed that that the SVGPath renders really small paths as bigger ellipses, around maybe 5 to 10 times bigger.. I looked at the svg image via inkscape and those ellipses don't appear. I created a javaFX project via Netbeans and included a running version and the source code. I hope it works like it does on my pc.
What I also noticed: One time I tried to reduce the among of paths via Inkscape and combined all country paths in the image and then those ellipses appeared too. I don't know whether it is relevant or a hint for the problem, but currently I have to manually delete those paths that appear as ellipses.

To see the differences, start the application and look at the svg image via inkscape. You will noticed alot of the Islands in the pacific and atlanic are rendered as ellipses.