What OS do you have? I have windows 7 and I had to run the installer in compatibility mode for windows XP before it worked correctly for me.

Seeing Mos Espa working fine in the editor it became evident that I just needed to navigate up to see the station and other assets on Strike at Parmel. So now I seem to have the map in okay, only issue now is that the only thing I can see properly are the Lambda Shuttles (the only statics which are not lightmapped, the station itself is really hard to see and the interior of the hangars and some of the platform is all that can really be seen. If I remove the object lightmap files and replace them with the original lightmap atlas file I can see everything clearly, so obviously there is some additional problem.

In Max I had to shift the sunlight asset up so the station was visible in that software, I wonder if that has had an effect or something? Maybe the light position in the editor has to be shifted up too? Though I thought that light was just directional so only the angle and direction should matter, the position shouldn't matter. A strange one for sure.

There is also the possible issue of needing an additional UV channel for the lightmaps, but this wasn't mentioned in the tutorial. I think that is only needed if an asset uses a tiled texture, which I suspect the station and most of the other assets do.

[EDIT:]

Hmmmm, looks like the Freighter and containers are showing up as expected, it is just the station which is playing up (most likely means the asset needs that second set of UVs for lightmapping due to a tiled texture being used. The lighting direction is okay, but perhaps needs to be raised so more light plays across the top of the assets (or angle of light changed to make it less shallow vertically).