Marching Cubes help

I''m working on a volumetric mesh generator for medical data. I read in the images voxelising them then I run the marching cubes algorithm on this to produce a mesh. I''ve now started producing meshes withing meshes by assigning different colours from the image a different isovalue. Then running it through the marching cubes algorithm multiple time starting from the lowest value and working up through the different isovalues to produce the different meshes. When the transition takes place from a colour to a background colour then it''s fine. When however when the transition is from one colour to another then the inner mesh is not formed properly. The mesh slants out the way and different layers do not meet up so there are holes in the mesh: http://students.dcs.gla.ac.uk/students/hanlonmj/temp/bmesh.JPG I''m using Paul Bourke''s Marching Cubes implementation: http://astronomy.swin.edu.au/~pbourke/modelling/polygonise/ Does anyone have any idea what could be cause this. I have tried multiple ways of doing this, ensuring that the shared borders are only produced once. Any help greatfully recieved. You can see sample data and the files produced by them at: http://students.dcs.gla.ac.uk/students/hanlonmj/temp