You might not have the speculars active. If your textures are named according to BC standards (i.e _glow on the diffuse maps), then all specular maps in NanoFX Model Viewer would have to be named _glow_spec to appear properly. I've often recommended to people porting ships/stations to the viewer, to remove the _glow suffix in the filenames, as it most often causes problems.
In short: A NanoFX-ified station will require that you rename the textures so that they don't have _glow in the filenames. For the rest, these are the required file-suffixes:
_spec = speculars
_norm / _normal = normal/bump maps
Station still looks great, but I think you might be currently seeing the viewer default "speculars", and not the model-specific specs.
EDIT: In your second image, it appears to be a straight line running straight through the mushroom-section of the station. The line covers the slanted "roof" area, all the way down to the edge of the mushroom. On the lefthand side of the image, near the blue windows. Unwelded vertices possibly, or NanoFX issue?