On linux there's a segfault on exit. valgrind reports something fishy going on in the MGH IO library, but isn't specific about what. If I disable setting the ITK_AUTOLOAD_PATH in Slicer3.cxx, the problem goes away, so it's probably something in the reader code.

int putSuccess
= vtkKWApplication::PutEnv(const_cast <char *> (itkAutoLoadPath.c_str()));
if (!putSuccess)
{
cout << "Unable to set ITK_AUTOLOAD_PATH. " << itkAutoLoadPath << endl;
}