While standing on a well lit cobble space outside at night, I noticed that the server was spiking badly on CPU (~130% with one player only vs ~ 60%-70% normally with multiple players). The effect stopped during the day, so I assumed it was a lighting issue.
After trying a few things like extinguishing fires and checking other areas that were well lit and full of entities and finding no problems, I realised that the problem area had a couple of saplings waiting to grow. When I accelerated that with bone meal, the second both of them were oak trees the CPU usage dropped sharply back to 50%
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Your Java is out of date. Please update your Java to the latest version: http://www.java.com/en/download/

Maybe you saw the "zombie lag" MC-17630 ?
Is this still a concern in the current Minecraft version? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.