Ok Marky - First of all nice model bro.
Now here's the scoop:
When exporting to MOD, the xporter takes all materials defined in the max file and automatically makes a single "Multi/Sub-Object" material named after the export file name, in this case "Commodore_Material". Import your MOD file that you sent me into MAX, then open the MAterial Editor. IGNORE ANY EXISTING MATERIALS CURRENTLY DISPLAYED IN THE MATERIAL EDITOR. Select "Get Material" button. Material Map Browser window appears. Select "Scene" radio button from the "Browse from" section. In the list display there should be "Commodore_Material" listed. Click and Drag that into a spot in the Material Editor window. A window will appear asking to instance or copy. Select instance, click ok. Select that Material. This is the model's material, not hte other individual materials that you were re-assigning to the model. Thats why the Saucer texture was mapped over the entire model.
Alrighty then, as you can see, the Multi/Sub Obect Material type is basically just a group of the materials that you defined in the MAX file, in this case 6 materials are in your group. Click on the first "Sub-Material", saucer top. This opens the suacer material, exactly like a regular material. Now open the Maps listing. See how the MOD Exporter has changed your maps from saucer top.jpg to saucer top.pcx?
I discovered two important things while experimenting:
1. All Material (Texture) Maps MUST be BMPs otherwise the MOD exporter plugin renames them to *.PCXs
2. YOU MUST export the MOD file into the same folder as your texture maps, otherwise the MOD exporter plugin renames them to *.PCXs, regardless if they are BMPs or not.
Now the SFC game engine will only accept BMPs or PCX texture maps, so JPGs wont work as far as I know. 3D studio does not seem to display PCXs so your pretty much stuck with BMP's. Of course, saving your textures as bmps will greatly increase the file size of the textures, but I think that you have enough room on your textures to get down to 3-4 texture/materials instead of 6. For instance, reduce the bridge texture and put it in the nacelle texture, or simply reduce its size to 256 or 512. Its a small part relative to the rest of the model, so quality will be unaffected. You could also reduce the BMP to 256 colors, Im very sure that would work though I have not experimented with this. Your illumination maps DEFINATELY need to be saved as 256 greyscale BMPS, color is not used in illumination maps so there is some savings in file size.
Anyway, in short It seems that you need to convert your maps to BMPs, change the materials in the material editor to use the BMPs, and export the MOD into the same folder. I converted your jpgs to bmps and exported into the same folder, and that worked.
Let me know if this works for you, it should - GOOD LUCK!