While this problem is rare, when world changes are saved to disk, Minecraft can pause briefly, causing a noticeable skip in the game. By default, Minecraft saves to disk every 900 ticks, and we have a snapshot script that runs hourly which also triggers a world save. There are 20 ticks per second (TPS) in a smoothly-running server, meaning that world saves should occur every 45 seconds or so.
CraftBukkit makes the auto-saves configurable and turns them off by default, as of RB 2377 (http://forums.bukkit.org/threads/craftb ... le.102934/). We recommend against also turning off the hourly snapshots, but if you are seeing a skipping problem every hour and wish for them to be disabled, please contact us (if you have a standard shared server) or set the number to 0 on your "managed panel" page (if you have a managed dedicated server).
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