Phantom unread message in Mail.app I have a smart mailbox with only one rule: messages that are unread.
Right now I have no unread messages in any of my acccounts, yet the smart mailbox shows a counter of 1.
Opening the smart mailbox shows no messages (this is correct). If a new message arrives, the counter goes up to 2, then as soon as I read that message it goes back to 1.
I tried:


Rebuilding my inboxes
Rebuilding my smart mailbox. Logs this error:



  27/10/13 11:42:18,753 Mail[16057]: * Assertion failure in
  +[MFLibrary mailboxIDForMailbox:loadIfNotPresent:], /SourceCache/Mail/Mail-1816/FrameworkTargets/MailFramework/Library/MFLibrary.m:9814
  Called on smart mailbox Unread (  0   MailCore
  0x00007fff8c6ecc8c -[MCAssertionHandler
  _handleFailureWithPreamble:description:arguments:] + 141  1   MailCore                            0x00007fff8c6ecafd -[MCAssertionHandler
  handleFailureInMethod:object:file:lineNumber:description:] + 215  2
  Mail                                0x00007fff8cdf105d +[MFLibrary
  mailboxIDForMailbox:loadIfNotPresent:] + 170  3   Mail
  0x00007fff8ce0ea24 -[MFLibraryStore
  rebuildTableOfContentsSynchronously] + 533   4   CoreFoundation                      0x00007fff921f3dec invoking + 140  5   CoreFoundation
  0x00007fff921f3c54 -[NSInvocation invoke] + 308   6   MailCore
  0x00007fff8c73db74 -[MCMonitoredInvocation invoke] + 211  7   MailCore
  0x00007fff8c760808 -[MCThrowingInvocationOperation main] + 40     8
  MailCore                            0x00007fff8c704f08
  -[MCInvocationOperation main] + 332  9   Foundation                          0x00007fff86da9591 -[_NSOperationInternal _start:] + 631   10 
  Foundation                          0x00007fff86da923b
  __NSOQSchedule_f + 64     11  libdispatch.dylib                   0x00007fff8f3212ad _dispatch_client_callout + 8     12  libdispatch.dylib
  0x00007fff8f3257ff _dispatch_async_redirect_invoke + 154  13 
  libdispatch.dylib                   0x00007fff8f3212ad
  _dispatch_client_callout + 8  14  libdispatch.dylib                   0x00007fff8f32309e _dispatch_root_queue_drain + 326     15 
  libdispatch.dylib                   0x00007fff8f324193
  _dispatch_worker_thread2 + 40     16  libsystem_pthread.dylib             0x00007fff8c3dfef8 _pthread_wqthread + 314  17 
  libsystem_pthread.dylib             0x00007fff8c3e2fb9 start_wqthread
  + 13 )



Deleting and recreating my smart mailbox
Adding a rule restricting the smart mailbox to one account (if the rule is added, it works correctly)
Relaunching mail, rebooting
Looking in the logs. Only line from mail: 27/10/13 11:38:19,956 Mail[1174]: View Based NSTableView error: preparedCellAtColumn:row: was called. Please log a bug with the backtrace from this log, or stop using the method. 


I'm kinda out of ideas. Is there anything else I can try, any debug info I can access?
I fixed this for my smart mailboxes (Mail.app v7.0 1822) by following these steps:


Open a terminal
Re-index Spotlight

sudo mdutil -E /


I suspect this is related to Mavericks improvements in Spotlight, as it now indexes Mail.app messages much better than in previous releases.