I am having the same issue when trying to sync with U1.

9/8/2011 8:01:42 AM [DEBUG]: Sync: 29 updates since rev -1
9/8/2011 8:01:42 AM [DEBUG]: SyncManager: Deleting auto-generated note: New 
Note Template
9/8/2011 8:01:42 AM [DEBUG]: Removing tag from New Note Template: 
system:template
9/8/2011 8:01:42 AM [DEBUG]: Watchers.OnTagRemoved popularity count: 0
9/8/2011 8:01:42 AM [DEBUG]: Deleting note 'New Note Template'.
9/8/2011 8:01:42 AM [DEBUG]: Creating Buffer for 'New Note Template'...
9/8/2011 8:01:42 AM [DEBUG]: Tag added to New Note Template: system:template
9/8/2011 8:01:42 AM [DEBUG]: Loading notebooks
9/8/2011 8:01:42 AM [ERROR]: Synchronization failed with the following 
exception: A note with this title already exists: New Note Template
  at Tomboy.NoteManager.CreateNewNote (System.String title, System.String 
xml_content, System.String guid) [0x00000] in <filename unknown>:0
  at Tomboy.NoteManager.CreateNoteFromTemplate (System.String title, 
Tomboy.Note template_note, System.String guid) [0x00000] in <filename unknown>:0
  at Tomboy.NoteManager.CreateNewNote (System.String title, System.String guid) 
[0x00000] in <filename unknown>:0
  at Tomboy.NoteManager.CreateWithGuid (System.String title, System.String 
guid) [0x00000] in <filename unknown>:0
  at Tomboy.Sync.SyncManager+<CreateNoteInMainThread>c__AnonStorey11.<>m__3F () 
[0x00000] in <filename unknown>:0
  at Tomboy.GuiUtils+<GtkInvokeAndWait>c__AnonStoreyC.<>m__2F (System.Object , 
System.EventArgs ) [0x00000] in <filename unknown>:0
9/8/2011 8:01:46 AM [DEBUG]: Saving 'New Note Template'...

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https://bugs.launchpad.net/bugs/848250

Title:
  Tomboy sync fails on Oneiric, New Note Template already exists

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