It just happened to me yesterday and again today. There were two chunks, as far as I know, the were replaced. Just I and a couple friends play, so not a whole lot lost. Had to rebuild a couple buildigs, now my whole "base" is issing a quarter of itself. lol I'd hate to visit the village lol. (spawn) I'm running the bukkit server on my self built pc. 4GB of Ram (upping to 8 here soon). 3.19GHz (not overclocked, just as is). 64bit Win7 Pro.
I have the exact same problem; http://forums.bukkit.org/threads/chunks-suddenly-getting-higher.899/#post-9947
