Confirmed on Hardy as well.  This is likely a result of the inotify
tracking of a save-via-new-file-and-rename.  For example, here is what
gnumeric does when saving:

access("/home/kees/Desktop/test.gnumeric", W_OK) = 0
open("/home/kees/Desktop/.gsf-save-68H34T", O_RDWR|O_CREAT|O_EXCL, 0600) = 14
rename("/home/kees/Desktop/.gsf-save-68H34T", 
"/home/kees/Desktop/test.gnumeric") = 0

The problem is that the desktop position of the new file is used,
instead of the position of the resulting filename.

-- 
Gnome desktop icons are shifted when the file is edited
https://bugs.launchpad.net/bugs/84262
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