I can confirm that this problem seems to exhibit itself when the Tomboy
program finishes loading before the gnome-panel does.  This happens
somewhat at random depending on how under load the start up session
currently is.  The more programs being loaded and tasks being performed,
the more likely the search dialog is to appear.

The other side effect is that closing this window causes the tomboy
instance to shutdown in the notification area as well.  Re-opening
tomboy again (e.g., alt+f2 and just doing 'tomboy' again) makes the
instance correctly load up and minimize to the notification area upon
close.

As a work around, I have made a quick shell script to delay the starting of 
tomboy by about 10s on start up. I've attached the startup script for the lazy. 
 It's contents are very simple:
#!/bin/sh
sleep $1
shift
exec $@

The script needs to be made executable, and then I simply put the command in 
session as:
/path/to/delay/file/delay 5 /usr/bin/tomboy

The first argument is the delay required, and the rest of the command
line is then passed to the exec process.


** Attachment added: "Short delay script"
   http://launchpadlibrarian.net/22998213/delay

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