When you import a *.mod into milkshape, it automatically has an emissive color of white. To make it look normal again, choose black for emissive. Now, when you export into *.mod format, "ambient," "specularity," "difuse," and "emissive" settings are all lost because the *.mod format does not support those features and the game has other ways of doing those. So, when you re-import it, the assimsolft plugin chooses these settings. You just have to go back and change them.