When you close the BOINC manager using the close button (X) it will
minimise to the tray in the desktop in which it was opened, and the tasks will continue to run. If you then try to launch the manager using an icon it will tell you the first one is still opened and ask if you wish to open a second one. Look in your tray in all your desktops and you should see it minimised. Open that one.
I seem to remember that it minimises itself after the first install. Close the manager in the menus under File. It will ask if you wish to close the window or exit the manager. Closing the window here minimises it same as with the close button. If you Exit the manager it will then ask if you wish to stop running the tasks. You can exit the manager but keep the tasks running, to save you some resources, or shut down the whole thing, as you wish.
You'll probably find that your menus disappear quite often in Kubuntu 12.04. If that happens just resize the window a few pixels and they will return. Don't ask me why...
Woof...