I think if you renamed the mat file as original mat from where you extract that... could work. Review the mat that you change, what ship you are changed?, don't forget that WCP use various panthers, vampires etc; and maybe you can not changing rigthly.
If you follow the procedure ship -> mesh -> mat exactly, that should've work.
Now as WCP use 3 cd's I don't know what can happen. I let a final response to experts.