(Using Kubuntu Karmic Alpha 2)
In have tomboy (0.15.0-0ubuntu1) sitting in my KDE (4.2.90) systray panel. When I log into KDE, tomboy's "Search All Notes" window is automatically shown, and when closing it the whole application quits (the systray icon disappears).
When I then manually start the application again by typing "tomboy" in the ALT+F2 run dialog, however, everything is as it should be: the systray icon appears, without the "Search All Notes" window popping up for no reason. Also now, when I manually open the "Search All Notes" window from the systray icon context menu, and then close it again, the application itself keeps running and the systray icon stays in place (as one would expect).
It's only on KDE startup when automatically restoring the previous session (which had tomboy running), that the peculiar behaviour occurs.
I'm not sure if this is related to the abandoned bug https://bugs.launchpad.net/ubuntu/+source/tomboy/+bug/240300, but unlike that user I use neither gnome nor a fingerprint scanner. Just KDE + normal kdm login; with everything from standard Ubuntu packages.
Correction:
It can also happen after starting tomboy manually through ALT-F2 or from a terminal. I can see no criteria whatsoever that might influence whether it happens or not. Sometimes, it just shows up nicely in the system tray; other times the ill-behaved search window pops up. (I tried quitting and restarting the application in different ways at least 10 times; the occurrence of the bug seems totally unpredictable to me.)
Another interesting fact is that the ill-behaved automatically-shown search window (should it come up) has no "Close" action in its "File" menu, only a "Quit" action, while a search window manually opened from a well-behaved tomboy instance has both menu entries.
When the problem occurs (i.e., the automatically shown ill-behaved search window is there), manually clicking "Search All Notes" from the systray icon context menu doesn't bring you a well-behaved search window either; it just raises the already opened ill-behaved one. It's as if the application randomly decided on start-up whether to behave this time or to be annoying ;-)