During imports of shapefiles and raster images files with coordinate systems, GDAL's OGRCreateCoordinateTransformation is called and fails. It fails due to a failure to dynamically load (via ::LoadLibrary) proj.dll.
Terrain Builder either needs to ship with proj.dll (or gdal needs to be compiled with the option to statically link it in).
These two issues are a result of the missing file:
http://feedback.arma3.com/view.php?id=18116
http://feedback.arma3.com/view.php?id=18081