This is happening because libunique calls gtk_window_present() on the
window inside of unique_app_real_message_received; whenever a second
Nautilus instance fires up, it sends the message to the running instance
and libunique "presents" the list of windows that it is watching again.
The "fix" is to remove the watch.

The following patch should do the trick:
Index: src/nautilus-application.c
===================================================================
--- src/nautilus-application.c  (revision 14859)
+++ src/nautilus-application.c  (working copy)
@@ -991,7 +991,6 @@
        /* Must be called after construction finished */
        nautilus_window_constructed (window);
 
-       unique_app_watch_window (application->unique_app, GTK_WINDOW (window));
        if (startup_id) {
                gtk_window_set_startup_id (GTK_WINDOW (window), startup_id);
        }

** Changed in: nautilus (Ubuntu)
   Importance: Undecided => Low
     Assignee: (unassigned) => Ubuntu Desktop Bugs (desktop-bugs)
       Status: New => Confirmed

-- 
[jaunty] nautilus sets urgent wm hint when not needed
https://bugs.launchpad.net/bugs/318629
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