Ok. So things seem to be fixed now.

Every time I ran the program to generate a new map, it told me what files had bad chunks.
I pulled out the bad .mcr region files and everything is better, but a few things are missing.

The biggest thing is the giant water tower that I think goat built. Sorry.
That whole area just got purged. Not sure how that chunk got bad.

I noticed a couple other small areas that are different, but not much that I can tell.

Here's the latest map:
http://www.lostpower.com/files/HAN-10-11-2011-FIXED.png

It's 18mb.


Let me know if you guys have any more problems.