Have you fiddled around with the Sh3Gen folder, particularly the camapign data? I ask because it looks like some part of the US East Coast data was added a second time.
Are you using the most recent version? If not, try this one:
http://www.global-explorer.de/Sh3Gen_v082.exe
This file also serves as an update to all people who had the problem with the new viewer version,
it should work with the new version of TatukGIS.
If not, somebody must let me know, as I am not doing full tests anymore - but it should work.