Old map got screwed over by chunk errors...hope there is a backup.
It appears that all the timeout issues I used to get have vanished now that qaz performed the item decimation on the entire map (including boats, minecarts, experience orbs, and floating items). The issues I have been plagued with since at least June 2011 appear to have been resolved.
That in mind, I heard that your place and JC's got chunk error'd. Did either of you have any mob grinders in those chunks, or perhaps did you die and lose a bunch of XP in that area? It's possible that XP orbs (which don't die in lava apparently) survived and piled up somehow (mobs used to drop XP from dying in grinders in one of the older versions (1.7.x perhaps?)). A pileup like that could have led to the item removal script/program qaz used to choke up when it tried parsing those chunks (just like Minecraft was apparently choking), resulting in an invalid - and thus regenerated from scratch - chunk. :-/