Comment 111 for bug 1335492

This bug is not fixed at all. There is a good chance reading icon positions from $HOME/.config/xfce4/desktop.conf is not finished before reading icons from $HOME/Desktop having icons rearrange. There is no locking nothing to make sure the icon positions are known BEFORE starting to read "Desktop".
And if this occurs the icons WILL again rearrange!
It will depend on how many applications you start, on IO-load, what is done in background. Processes reading many small files from disk, like man-page-updates, can trigger it.
A fast look at what the code does made clear: you do not have anything making sure the two threads: read "Desktop", read "Config" are not forced to run after each other. The part positioning the icons isn't locked at all. It will run concurrently to read config if read desktop is finished. It is triggered every time an item is read from read Desktop -- regardless reading configs is ready or not.