Skinned Mesh Renderer Combining submesh issue

I am having an issue with combining skinned mesh renderers into one single mesh. One mesh has two submeshes in it and the other mesh has just one. When I combine them, I get the first submesh of the first mesh and the mesh of the second object to combine correctly, but the second submesh of the first mesh disappears. The instance mesh in the inspector shows 3 submeshes and has the same vertex count as both separate meshes have in total, so it has to be there somewhere.

I am using CombineInstance method

"sharedMesh.CombineMeshes( m_combineInstances.ToArray(), false, false );"

to do so and I have the sharedMesh.subMeshCount equal to the total amount, 3 in this case, and I have plugged in 3 materials into the renderer after the mesh is combined.

Am I missing something?

I did more digging and think it has to do something with the subMeshIndex on the combineinstance node but the best I get is getting either is one of either of the two submeshes. If I try to duplicate the combineindex and change the submeshindex to the other index and then combine them, I double the vertex count and it breaks the rest of my code.