Server Announcement
I tracked down the time problem to the server being at full (100%) memory load all of the time. Since there was no more memory to work with the world appears laggy and ticks are not being processed the way they should.
Since this is often a plugin issue, I started to isolate all the plugins one by one and have narrowed it down to the plugin responsible. Which unfortunately is the Dynmap plugin that provided that fancy map I posted earlier. Apparently it is too resource intensive to run on our small server so I have disabled it. As such the map itself is not available anymore either, which is a shame.
The server runs smooth again now though and is running at about 75% memory. Hope this fixes all issues. There should also be a new Craftbukkit build for Minecraft 1.4.4 soon. Currently there is only an unstable Dev build.