Are you using the correct shader? It should be "PdxMeshShip" or "PdxMeshTerra".
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You can find them if you select your phong shader in the hypershader, go to the channel box, at the bottom of the attribute list there should be an attribute named "shader" if you have added it through the exporter. There you should have a drop down menu of different shader options. These however may not correspond with the game that you are exporting to so you may need to change them to whatever is appropriate for the game you are modding.Where are these options suppose to be? I applied a phong material as the wiki guide says to and that guide makes no mention of PdxMeshShip or PdxMeshTerra.