I have the same issue with SH3Gen too: no terrain detail on the GIS map. I think there might be a terrain.exe file from Global Explorer that updates the terrain files for use with TatukGIS, but it's not available anymore from Global Explorer's website.
First post below mentions a terrain.exe file to download to fix this:
http://www.subsim.com/radioroom/show...h3gen&langid=5