I did a similar thing. Its a bit more complicated. If, for example, you want to have the hawk classed civilian ship with a different texture. You download the mat file, change shiparch and baseside everything is mostly ok.
The problem is that inside the mat file, the names of the textures are same. They need to be for the texture to work, but by doing so causes the problem. If the computer sees a falcon first it loads up the mat file, adds the crc's (i guess), loads the textures in to memory, you see the ship.
Then your hawk comes along, it looks at either the mat file or the cmp and see's the same named entries and dosen't load the actual textures. It does a shortcut to increase performance and uses the already used textures which it assumes is ok.

The only way to get around the problem is to either use model cloner (its probably ok, but i had trouble doing capital ships) or by importing the model into milkshape, assigning each group a unique name, renaming the textures too and adding hardpoints. If you go the milkshape way, the ship will lose the separable objects, so its best to have a go at using model cloner. I haven't heard of anybody else having problems with it, so its probably just me being clumsy.

Well, I couldn't get the cloner to work either at first. I'll keep trying though - Thanks!