I know this thread is a bit old, but have you fixed it yet?
I can look at the files for you if you like.
Black and yellow skin of the exported MD3?
No1_sonuk
(No1_sonuk)
#1
_NOB_Perica
(*NOB* Perica)
#2
Yeah I fixed it long time ago but thx for the help!
Actually, I’m using Npherno’s MD3 compiler and the patch in the QC file (generated by Milkshape) have to be correct. 
Jaquboss
(Jaquboss)
#5
That´s all?!
Well i must get md3 improter with anim and tag support and try to enhance models …
No1_sonuk
(No1_sonuk)
#6
Yup, the MD3 exporter has a checkbox that says something like “use the material name as the shader path”. It should be checked by default.