Looking again at the code, it's clearly what it seek for (that's the part of code I've changed recently):
1 - loading home/desktop/examples/downloads (the later only if examples.desktop is present in your home)
2 - looking at nautilus bookmark, and if there is home/desktop/downloads, ignore them :/
What do you have in your .gtk-bookmarks?
Looking again at the code, it's clearly what it seek for (that's the part of code I've changed recently): examples/ downloads (the later only if examples.desktop is present in your home) downloads, ignore them :/
1 - loading home/desktop/
2 - looking at nautilus bookmark, and if there is home/desktop/
What do you have in your .gtk-bookmarks?