I did select all and apply to all when I was testing the material thats probably the problem. When you "apply to all" it does not delete the nodes out of the other material zones before adding the new ones. You should be able to fix this by applying your material, holding down shift and hitting the wacro and then resaving the material. I have had the "removed detached nodes" not delete all the nodes (especialy image nodes) so you may double check your zones before resaving.

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