Thanks for the reply.
I currently use 2013.1 (had the issue with 2012.x but waited for 2013.1 before reporting it, in case it was already fixed).
I attached a file exhibiting the issue (with generated fbx output).
In the Maya scene, Outdoor and Outdoor_2 both have DiffuseColor pointing to layeredTexture3 (which points to 3 textures).
When you export (in my example I exported pCube1 and pCube2), inside the resulting FBX file, Outdoor points to layeredTexture3 as expected, but Outdoor_2 points to one of the subtexture of layeredTexture3 instead of layeredTexture3 itself.
;LayeredTexture::layeredTexture3, Material::Outdoor
C: "OP",319888848,1434779232, "DiffuseColor"
;Texture::file24, Material::Outdoor_2
C: "OP",307318032,1434778832, "DiffuseColor"
Please feel free to ask if you need more info!
hypergraph_share.zip