Sounds to me as though you used a stock model, but swapped over the texture from another model to get the colours you wanted. This doesn't always work for a variety of reasons!

The square shield is a result of the alpha texture not being in the same place as the shield UV map...I would guess the shield itself looked wrong.

The only cure is to do a completely new texture based on the one ariginally applied to the model, or else you are going to have to re-map the thing.