Multiple geometry files in a Atlas file

I would like to be able to load more than one geometry file from a single atlas file and I am running into some trouble.

I setup a custom console function to create the atlas file similar to atlasGenerateBlenderTerrain like so

Con::printf("   o Opening '%s' for geometry...", argv[2]);
   inGeometryFile = AtlasFile::load(argv[2]);
   if(inGeometryFile.isNull())
   {
      Con::errorf("atlasGenerateMultiBlenderTerrain - unable to open '%s' for input!", argv[2]);
      return false;
   }

   /*   Con::printf("   o Opening '%s' for geometry...", argv[3]);
   inGeometryFile2 = AtlasFile::load(argv[3]);
   if(inGeometryFile2.isNull())
   {
      Con::errorf("atlasGenerateMultiBlenderTerrain - unable to open '%s' for input!", argv[3]);
      return false;
   }*/

........
........

   // First Geometry .
   AtlasResourceGeomTOC *originalArgtoc = NULL;
   if(!inGeometryFile->getTocBySlot(0, originalArgtoc))
   {
      Con::errorf("atlasGenerateMultiBlenderTerrain - inGeometryFile does not have a Geometry TOC.");
      return false;
   }

   AtlasResourceGeomTOC *argtoc = new AtlasResourceGeomTOC;
   argtoc->copyFromTOC(originalArgtoc);
   outFile.registerTOC(argtoc);

   // Second Geometry .
   AtlasResourceGeomTOC *originalArgtoc2 = NULL;
   if(!inGeometryFile2->getTocBySlot(0, originalArgtoc2))
   {
      Con::errorf("atlasGenerateMultiBlenderTerrain - inGeometryFile does not have a Geometry TOC.");
      return false;
   }

   AtlasResourceGeomTOC *argtoc2 = new AtlasResourceGeomTOC;
   argtoc2->copyFromTOC(originalArgtoc2);
   outFile.registerTOC(argtoc2);

This is not all the code but it is the part that was added.
It basically loads a second atlas file containing the additional set of data I want to use and uses outFile.registerTOC to add it to the atlas file.
The function goes on to add the lightmap and opacity data as well , just like a regular blended atlas file.

The problem I run into is when I try to load the atlas file like AtlasInstance::onAdd() loads the first geometry and it fails to read the second one correctly and errors out.

This is the relevent code in AtlasInstance::onAdd()

//first geom
   AtlasResourceGeomTOC   *argtoc=NULL;
   mAtlasFile->getTocBySlot(0, argtoc);
   mGeomTOC = new AtlasInstanceGeomTOC;
   mGeomTOC->initializeTOC(argtoc);

//second geom
   AtlasResourceGeomTOC   *argtoc2=NULL;
   mAtlasFile->getTocBySlot(1, argtoc2);
   mGeomTOC2 = new AtlasInstanceGeomTOC;
   mGeomTOC2->initializeTOC(argtoc2);

It fails at mGeomTOC2->initializeTOC(argtoc2); and says that it got an invalid sentinal chunk.
After a debug session it appears it is loading data from the wrong part of the atlas file and spits out an error.
The odd thing is if I change the loading of the second geom file in the onAdd function to load from a seperate atlas file it works fine.

So my question is , Am I simple doing it wrong or is this not possible with the atlas system right now.