This is taken straight from the milkshape forums - I don't think it's what you're encountering, but it might work...
Quote: "1. This works most of the time select all, go to the Groups tab and make sure Auto Smooth is checked in the groups options. Use the menu commands Vertex-> Unweld. Uncheck the the Auto Smooth in the groups options. Use the menu commands Vertex->Weld
2. If the above didnt fix it, first regroup the problem groups and apply the same steps above. (Dont know why you have to do this as well sometimes)."