The lag should be fixed now I think. Believe it or not, it was Bukkit causing it...the latest Bukkit recommended build. The description for a build that came two builds after the recommended one we were running pretty much explains it:

Quote Originally Posted by http://dl.bukkit.org/downloads/craftbukkit/view/01335_1.3.1-R1.1/
Make periodic chunk saving less aggressive and fixed double player data saving.
Emphasis mine. Herp derp...