Same issue here. Noticed it because the notification message was complaining about a file in a directory for the last few days so I tarred it all up but still get the message regarding the new file.

I have rebooted between and my machine has been offline for the weekend (work PC).

I went digging in the logs and found this relevant line:

ubuntuone.SyncDaemon.StorageClient - INFO - Connection lost, reason: [Failure instance: Traceback (failure with no frames): <class 'OpenSSL.SSL.Error'>: [('SSL routines', 'SSL23_READ', 'ssl handshake failure')]

Hmm ... after poking and prodding it things have come right - but all I've done is look at the log file and use the Ubuntu One GUI to stop and start the system. I wonder if this is server load related. Here is something odd from the log file that may help with diagnosis of future instances of this:

2012-02-27 09:53:48,258 - ubuntuone.SyncDaemon.ActionQueue - INFO - Connection started to host fs-1.ubuntuone.com, port 443.
2012-02-27 09:53:48,793 - ubuntuone.SyncDaemon.ActionQueue - INFO - Connection made.
2012-02-27 09:53:48,793 - ubuntuone.SyncDaemon.StorageClient - INFO - Connection made.
2012-02-27 09:53:49,754 - ubuntuone.SyncDaemon.ActionQueue - INFO - The request 'protocol_version' finished OK.
2012-02-27 09:53:50,065 - ubuntuone.SyncDaemon.ActionQueue - INFO - The request 'caps_raising_if_not_accepted' finished OK.
2012-02-27 09:53:50,375 - ubuntuone.SyncDaemon.ActionQueue - INFO - The request 'caps_raising_if_not_accepted' finished OK.
2012-02-27 09:53:50,697 - ubuntuone.SyncDaemon.ActionQueue - INFO - The request 'oauth_authenticate' finished OK.
2012-02-27 09:53:50,697 - ubuntuone.SyncDaemon.ActionQueue - NOTE - Session ID: 'ab291d74-904b-4acd-a136-0543033ce6c6'
2012-02-27 09:54:52,184 - ubuntuone.SyncDaemon.Main - NOTE - ---- MARK (state: <State: 'SERVER_RESCAN'  (queues WORKING  connection 'With User With Network')>; queue: 91; hash: 0) ----
2012-02-27 09:55:51,916 - twisted - ERROR - Unhandled Error
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/twisted/python/log.py", line 84, in callWithLogger
    return callWithContext({"system": lp}, func, *args, **kw)
  File "/usr/lib/python2.7/dist-packages/twisted/python/log.py", line 69, in callWithContext
    return context.call({ILogContext: newCtx}, func, *args, **kw)
  File "/usr/lib/python2.7/dist-packages/twisted/python/context.py", line 118, in callWithContext
    return self.currentContext().callWithContext(ctx, func, *args, **kw)
  File "/usr/lib/python2.7/dist-packages/twisted/python/context.py", line 81, in callWithContext
    return func(*args,**kw)
--- <exception caught here> ---
  File "/usr/lib/python2.7/dist-packages/twisted/internet/gtk2reactor.py", line 288, in _doReadOrWrite
    why = source.doRead()
  File "/usr/lib/python2.7/dist-packages/twisted/internet/tcp.py", line 137, in doRead
    return Connection.doRead(self)
  File "/usr/lib/python2.7/dist-packages/twisted/internet/tcp.py", line 460, in doRead
    rval = self.protocol.dataReceived(data)
  File "/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol/ubuntuone/storageprotocol/client.py", line 1601, in dataReceived
    StorageClient.dataReceived(self, data)
  File "/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol/ubuntuone/storageprotocol/client.py", line 91, in dataReceived
    request.RequestHandler.dataReceived(self, data)
  File "/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol/ubuntuone/storageprotocol/request.py", line 143, in dataReceived
    self.buildMessage(data)
  File "/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol/ubuntuone/storageprotocol/request.py", line 190, in buildMessage
    self.processMessage(message)
  File "/usr/lib/python2.7/dist-packages/ubuntuone-client/ubuntuone/syncdaemon/action_queue.py", line 272, in processMessage
    result = ThrottlingStorageClient.processMessage(self, message)
  File "/usr/lib/python2.7/dist-packages/ubuntuone-storage-protocol/ubuntuone/storageprotocol/request.py", line 232, in processMessage
    str(message).replace("\n", " ")))
exceptions.Exception: peer cant handle message 'ERROR' {id: 7 type: ERROR error {   type: TRY_AGAIN   comment: "TryAgain (RPCTimeoutError: )" } }

2012-02-27 09:55:51,916 - ubuntuone.SyncDaemon.StorageClient - INFO - Connection lost, reason: [Failure instance: Traceback (failure with no frames): <type 'exceptions.Exception'>: peer cant handle message 'ERROR' {id: 7 type: ERROR error {   type: TRY_AGAIN   comment: "TryAgain (RPCTimeoutError: )" } }
].
2012-02-27 09:55:51,917 - ubuntuone.SyncDaemon.ActionQueue - WARNING - Connection lost: peer cant handle message 'ERROR' {id: 7 type: ERROR error {   type: TRY_AGAIN   comment: "TryAgain (RPCTimeoutError: )" } }