I just did some looking into this one.  I was able to duplicate this bug
by launching Tomboy after it was already launched.  If Tomboy is already
running it will cause the search to come up the second time.  Also, the
default Ubuntu (gnome) menu launches "tomboy --search" and will always
load the search and the tray as well.

I'm not running Xubuntu so it's difficult to completely duplicate your
settings but I would agree with Sean above.  If you are saving your
session changes *and* auto loading the tomboy app it may be trying to
load it twice.  If you try just one or the other does it persist?  Can
you validate that the 'sometimes' it loads the search are the times that
it is running when you close the session and re-open the session?

-- 
tomboy sometimes starts with search dialog rather than as minimized applet
https://bugs.launchpad.net/bugs/112703
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