Weird XDG User Dir resetting bug
There exists an autostart script
/etc/xdg/autostart/user-dirs-update-gtk.desktop
Which calls the program xdg-user-dirs-gtk-update, which appears to have no man page or --help explanation, but I am guessing might be the cause.
You can either delete this script (which appears to belong to the package xdg-user-dirs-gtk, and may be recreated if it is updated), or add a line Hidden=true to the autostart file, which should prevent it running (and you should be asked if you want to keep your modified copy during any future updates).