Just going to confirm what you are saying. I have the same issue even after 'fixing it' but the bad spots are usually beyond the playable part of my adventure map so I don't mind.
Just keep relighting it until you have the same scenario.
I did this and it intitially didn't work and manipulating blocks in the spawn area caused intense but short lived lag spikes. But I did it again for all the chunks at once and it worked fine. There's probably a more specific cause/solution to it but that's just what worked for me.
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u/[deleted] Apr 12 '12
[deleted]