Sorry I'm too late, but you figured it out anyway! I just hope this stays intact for whenever Bukkit merges (I'm assuming since they are part of Mojang now) with the official Minecraft builds.
I had the same problem with my Nether resetting on the update, but I re-started the server with the latest Bukkit build and my Nether was back. Most of the plugins didn't work, but I'm ok with that for now.
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