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I also suspect problems with network connectivity. Some systems seem to send one last message before realizing that the connection has been dropped. (Especially when VPN’s are involved.)
Alternatively, you could have received and ack’d a message that was lost through “configuration error”, like Michael said. Are you using the recovery database all the way through? Even on newly created messages? Is there any proc that could KILL a message when it should have been CONTINUED?
It could be missing from SMAT because someone was viewing the smat files while the thread was starting up, or drive space could have been low enough that the threads automatically stopped saving. Or, if the machine was power cycled, I imagine the SMAT file buffers could have been lost. (I don’t know if SMAT files are sync’d on write or not.)