When I wrote the first post, I get this in my debug file: 
** Running Mono with --debug    **
[DEBUG 23:08:53.965] NoteManager created with note path 
"/home/coolben/.local/share/tomboy".
[INFO 23:08:54.498] Initializing Mono.Addins
[DEBUG 23:08:54.569] AddinManager.OnAddinLoaded: Tomboy.Tomboy
[DEBUG 23:08:54.570]           Name: Tomboy.Tomboy,0.10
[DEBUG 23:08:54.570]    Description: 
[DEBUG 23:08:54.570]      Namespace: Tomboy
[DEBUG 23:08:54.570]        Enabled: True
[DEBUG 23:08:54.570]           File: /usr/lib/tomboy/Tomboy.exe
[DEBUG 23:08:55.321] AddinManager.OnAddinLoaded: Tomboy.ExportToHtmlAddin
[DEBUG 23:08:55.321]           Name: Export to HTML
[DEBUG 23:08:55.321]    Description: Exports individual notes to HTML.
[DEBUG 23:08:55.321]      Namespace: Tomboy
[DEBUG 23:08:55.321]        Enabled: True
[DEBUG 23:08:55.321]           File: /usr/lib/tomboy/addins/ExportToHtml.dll
[DEBUG 23:08:55.325] AddinManager.OnAddinLoaded: Tomboy.WebSyncServiceAddin
[DEBUG 23:08:55.325]           Name: Web Sync Service Add-in
[DEBUG 23:08:55.325]    Description: Synchronize Tomboy Notes with Tomboy 
Online and other compatible web services
[DEBUG 23:08:55.325]      Namespace: Tomboy
[DEBUG 23:08:55.325]        Enabled: True
[DEBUG 23:08:55.325]           File: 
/usr/lib/tomboy/addins/WebSyncServiceAddin.dll
[DEBUG 23:08:55.326] AddinManager.OnAddinLoaded: Tomboy.WebDavSyncServiceAddin
[DEBUG 23:08:55.326]           Name: WebDav Sync Service Add-in
[DEBUG 23:08:55.326]    Description: Synchronize Tomboy Notes to a WebDav URL
[DEBUG 23:08:55.326]      Namespace: Tomboy
[DEBUG 23:08:55.326]        Enabled: True
[DEBUG 23:08:55.326]           File: 
/usr/lib/tomboy/addins/WebDavSyncService.dll
[DEBUG 23:08:55.328] Unable to locate 'gnomesu' in your PATH
[DEBUG 23:08:55.329] Using '/usr/bin/gksu' as GUI 'su' tool
[DEBUG 23:08:55.329] Successfully found all system tools
[DEBUG 23:08:55.329] Unable to locate 'wdfs' in your PATH
[DEBUG 23:08:55.329] AddinManager.OnAddinLoaded: 
Tomboy.FileSystemSyncServiceAddin
[DEBUG 23:08:55.329]           Name: Local Directory Sync Service Add-in
[DEBUG 23:08:55.329]    Description: Synchronize Tomboy Notes to a local file 
system path
[DEBUG 23:08:55.329]      Namespace: Tomboy
[DEBUG 23:08:55.329]        Enabled: True
[DEBUG 23:08:55.329]           File: 
/usr/lib/tomboy/addins/FileSystemSyncService.dll
[DEBUG 23:08:55.333] Loading notes
[DEBUG 23:08:55.645] AddinManager.OnAddinLoaded: Tomboy.StickyNoteImportAddin
[DEBUG 23:08:55.646]           Name: Sticky Notes Importer
[DEBUG 23:08:55.646]    Description: Import your notes from the Sticky Notes 
applet.
[DEBUG 23:08:55.646]      Namespace: Tomboy
[DEBUG 23:08:55.646]        Enabled: True
[DEBUG 23:08:55.646]           File: /usr/lib/tomboy/addins/StickyNoteImport.dll
[DEBUG 23:08:55.647] StickyNoteImporter: Sticky Notes XML file does not exist 
or is invalid!
[DEBUG 23:08:55.647] AddinManager.OnAddinLoaded: Tomboy.BacklinksAddin
[DEBUG 23:08:55.647]           Name: Backlinks
[DEBUG 23:08:55.647]    Description: See which notes link to the one you're 
currently viewing.
[DEBUG 23:08:55.647]      Namespace: Tomboy
[DEBUG 23:08:55.647]        Enabled: True
[DEBUG 23:08:55.647]           File: /usr/lib/tomboy/addins/Backlinks.dll
[DEBUG 23:08:55.648] AddinManager.OnAddinLoaded: Tomboy.EvolutionAddin
[DEBUG 23:08:55.648]           Name: Evolution Mail Integration
[DEBUG 23:08:55.648]    Description: Allows you to drag an email from Evolution 
into a Tomboy note.  The message subject is added as a link in the note with an 
envelope icon next to it.
[DEBUG 23:08:55.648]      Namespace: Tomboy
[DEBUG 23:08:55.649]        Enabled: True
[DEBUG 23:08:55.649]           File: /usr/lib/tomboy/addins/Evolution.dll
[DEBUG 23:08:55.651] AddinManager.OnAddinLoaded: Tomboy.PrintNotesAddin
[DEBUG 23:08:55.651]           Name: Printing Support
[DEBUG 23:08:55.651]    Description: Allows you to print a note.
[DEBUG 23:08:55.651]      Namespace: Tomboy
[DEBUG 23:08:55.651]        Enabled: True
[DEBUG 23:08:55.651]           File: /usr/lib/tomboy/addins/PrintNotes.dll
[DEBUG 23:08:55.652] AddinManager.OnAddinLoaded: Tomboy.FixedWidthAddin
[DEBUG 23:08:55.652]           Name: Fixed Width
[DEBUG 23:08:55.652]    Description: Adds fixed-width font style.
[DEBUG 23:08:55.653]      Namespace: Tomboy
[DEBUG 23:08:55.653]        Enabled: True
[DEBUG 23:08:55.655]           File: /usr/lib/tomboy/addins/FixedWidth.dll
[DEBUG 23:08:55.760] Unable to locate 'wdfs' in your PATH
[DEBUG 23:08:55.763] Autosync pref changed...restarting sync timer
[DEBUG 23:08:55.782] Tomboy remote control active.
[DEBUG 23:08:59.131] SyncThread using SyncServiceAddin: Tomboy Web
[DEBUG 23:08:59.155] Building web request for URL: 
https://one.ubuntu.com/notes/api/1.0/
[DEBUG 23:09:00.675] Building web request for URL: 
https://one.ubuntu.com/notes/api/1.0/user/
[ERROR 23:09:00.994] Caught exception. Message: The remote server returned an 
error: (500) INTERNAL SERVER ERROR.
[ERROR 23:09:00.998] Stack trace for previous exception:   at 
System.Net.HttpWebRequest.CheckFinalStatus (System.Net.WebAsyncResult result) 
[0x00000] in <filename unknown>:0 
  at System.Net.HttpWebRequest.SetResponseData (System.Net.WebConnectionData 
data) [0x00000] in <filename unknown>:0 
[ERROR 23:09:01.002] Rest of stack trace for above exception:    at 
System.Environment.get_StackTrace()
   at Tomboy.WebSync.Api.OAuth.MakeWebRequest(RequestMethod method, 
System.String url, System.Collections.Generic.List`1 parameters, System.String 
postData)
   at Tomboy.WebSync.Api.OAuth.WebRequest(RequestMethod method, System.String 
url, System.String postData)
   at Tomboy.WebSync.Api.OAuth.Get(System.String uri, IDictionary`2 
queryParameters)
   at Tomboy.WebSync.Api.UserInfo.GetUser(System.String userUri, IWebConnection 
connection)
   at Tomboy.WebSync.WebSyncServer.BeginSyncTransaction()
   at Tomboy.Sync.SyncManager.SynchronizationThread()
   at System.Threading.Thread.StartInternal()
[ERROR 23:09:01.003] Synchronization failed with the following exception: The 
remote server returned an error: (500) INTERNAL SERVER ERROR.
  at System.Net.HttpWebRequest.CheckFinalStatus (System.Net.WebAsyncResult 
result) [0x00000] in <filename unknown>:0 
  at System.Net.HttpWebRequest.SetResponseData (System.Net.WebConnectionData 
data) [0x00000] in <filename unknown>:0 
[DEBUG 23:09:09.507] Quitting Tomboy.  Ciao!
[DEBUG 23:09:09.515] Saving unsaved notes...

Today, I can synchronize with Ubuntu One.
And I change nothing about tomboy on my computer except i download and install  
update packet for my ubuntu system.

I hope this can help you

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https://bugs.launchpad.net/bugs/996907

Title:
  Tomboy notes failed to synchronise,  (500) INTERNAL SERVER ERROR.

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