I can reproduce this issue with

 * Ubuntu Hardy Heron 8.04 32-bit
 * Tomboy 0.10.2
 * Tomfox Firefox Addon  1.0.2

So it's more a bug inside tomboy and not GNOME Do...

When i create a tomboy note via Tomfox Tomboy is started within the notification area even though it is allready active as a panel applet. Here's mine ~/.tomboy.log when I add Tomboy to the panel as a applet.

$ tail -f -n 0 ~/.tomboy.log
tail: /home/toff/.tomboy.log: Datei abgeschnitten
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.EvolutionAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: Evolution Mail Integration
27.09.2008 22:16:25 [DEBUG]: 	Description: Allows you to drag an email from Evolution into a tomboy note.  The message subject is added as a link in the note.
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/Evolution.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.PrintNotesAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: Printing Support
27.09.2008 22:16:25 [DEBUG]: 	Description: Allows you to print a note.
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/PrintNotes.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.BacklinksAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: Backlinks
27.09.2008 22:16:25 [DEBUG]: 	Description: See which notes link to the one you're currently viewing.
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/Backlinks.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.FixedWidthAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: Fixed Width
27.09.2008 22:16:25 [DEBUG]: 	Description: Adds fixed-width font style.
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/FixedWidth.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.ExportToHtmlAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: Export to HTML
27.09.2008 22:16:25 [DEBUG]: 	Description: Exports individual notes to HTML.
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/ExportToHtml.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.StickyNoteImportAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: Sticky Notes Importer
27.09.2008 22:16:25 [DEBUG]: 	Description: Import your notes from the Sticky Notes applet.
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/StickyNoteImport.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.SshSyncServiceAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: SSH Sync Service Add-in
27.09.2008 22:16:25 [DEBUG]: 	Description: Synchronize Tomboy Notes to a SSH share
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/SshSyncServiceAddin.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.WebDavSyncServiceAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: WebDav Sync Service Add-in
27.09.2008 22:16:25 [DEBUG]: 	Description: Synchronize Tomboy Notes to a WebDav URL
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/WebDavSyncService.dll
27.09.2008 22:16:25 [DEBUG]: AddinManager.OnAddinLoaded: Tomboy.FileSystemSyncServiceAddin
27.09.2008 22:16:25 [DEBUG]: 	       Name: Local Directory Sync Service Add-in
27.09.2008 22:16:25 [DEBUG]: 	Description: Synchronize Tomboy Notes to a local file system path
27.09.2008 22:16:25 [DEBUG]: 	  Namespace: Tomboy
27.09.2008 22:16:25 [DEBUG]: 	    Enabled: True
27.09.2008 22:16:25 [DEBUG]: 	       File: /usr/lib/tomboy/addins/FileSystemSyncService.dll
27.09.2008 22:16:25 [DEBUG]: Unable to locate 'gnomesu' in your PATH
27.09.2008 22:16:25 [DEBUG]: Using '/usr/bin/gksu' as GUI 'su' tool
27.09.2008 22:16:25 [DEBUG]: Successfully found all system tools
27.09.2008 22:16:25 [DEBUG]: Unable to locate 'sshfs' in your PATH
27.09.2008 22:16:25 [DEBUG]: Unable to locate 'wdfs' in your PATH
27.09.2008 22:16:26 [DEBUG]: Tomboy remote control disabled (DBus exception): Unable to open the session message bus.
27.09.2008 22:16:26 [DEBUG]: Applet Created...
27.09.2008 22:16:26 [DEBUG]: EnableDisable Called: enabling... True
27.09.2008 22:16:26 [DEBUG]: Binding key '<Alt>F12' for '/apps/tomboy/global_keybindings/show_note_menu'
27.09.2008 22:16:26 [DEBUG]: Binding key '<Alt>F11' for '/apps/tomboy/global_keybindings/open_start_here'