Alright I've found some potential issues that you could fix for your model to work better!
When you're using the Paradox exporter you have to use the animation attribute on the root joint, which you do. However you need to separate the animations either by a new animation or by the attribute "none" to close an animation (you can add this by selecting the root joint and then go to Modify > Edit attribute.). You can also use different materials for different meshes, you need to set the PdxMeshShip shader on each of them.
When skinning the mesh you have to bind the skin to the root joint (highest in hierarchy) to each of the meshes, then paint the skin weights for each mesh to use the desired weights for each joint. For your model it's probably going to be 0 on every joint and 1 on the correct joint for that mesh.
Modeling pointers:
1. Textures are way too big for the level of detail on the model. Compare with the texture resolution of our battleships for example. If you will add much more detail to the texture then it might be reasonable to keep them at 2048x2048.
2. Use much more texture tiling.
3. Use plating details in normal map, this includes indents and edges.