I figured out the issue since my SK mesh had two materials (one for the head, one for the body). The base mesh was using the correct body material for the body and head material for the head. However, the LOD01 meshes and plus was using the body material for the head and head material for the body. So if you click on each LOD and look at the editor on the left, just click on the material settings and switch them around, they should look like as they should like the base mesh. Geez, who knew such an odd problem could be just simple misunderstanding and fixed easily.