Comment 3 for bug 793257

The applet doesn't create or delete folders. It only monitors whether the special XDG folders (in the following order: Documents, Music, Pictures, Videos, Downloads, Public, Templates) and your local (non-remote) bookmarks exist. If they exist, then it shows an icon for them. If the applet detects you or another application removed a special XDG folder or bookmarked local folder, then it hides the corresponding icon.

So it displays an icon for your home folder, your desktop, the special XDG folders (only those that exist in your home folder) and then your bookmarks (for local bookmarks only those that exist -- remote ones are always displayed) If one of your bookmarks is in fact a special XDG folder, then it ignores it (to avoid duplicates)

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If I look at the position of the unwanted user/home icons, then they seem to correspond with: Documents, Music, and Downloads. You removed Documents, and Music. And then those icons disappeared in the applet if I understand you correctly, leaving only Downloads to remain.

That makes me think that something created Downloads because the applet shouldn't show an icon for it if the folder doesn't exist.

Can you open a terminal and then start "python". Then type:

import glib
print glib.get_user_special_dir(glib.USER_DIRECTORY_DOWNLOAD)
print glib.get_user_special_dir(glib.USER_DIRECTORY_MUSIC)
print glib.get_user_special_dir(glib.USER_DIRECTORY_DOCUMENTS)
print glib.get_user_special_dir(glib.USER_DIRECTORY_PICTURES)

Just type each line and then press enter, the prints should print the path to the directory.