Just a note, the importing of milkshape does not work for animations. It works for material files, meshes, skeletons, but in milkshape, animations are stored in the materials array. EE editor is bringing them in as material files, not as animations. I suggest (at least) updating the documentation that EE editor does not import milkshape animations. If I can provide any files to help extend the functionality of EE, please let me know. (persionally, I have a complete workaround, just mentioning to help the engine mature)
There is a section in milkshape called materials. If you have multiple animations in one ms3d file, you can store them all in this array.
EE editor doesn't parse these files correctly, and auto-assumes that they are all materials. (I'm not saying it's the best way to do things but that's how some models are)
It would be nice to have EE editor parse that out. (As I said, I have a workaround - just trying to help the engine a bit)