Kid, if I'm following your question correctly, I ran into the same thing with my 3-shuttle bash. I did it by saving in stages, like this:
1) opened the model in question ("shtl"), selected, copied, pasted; then saved it under a new name, i.e. "shtl_x2"
2) opened "shtl" again, selected, copied.
5) opened "shtl_x2", pasted another shuttle, saved as "shtl_x3"
Is this what you meant?
BTW,how does the community at large feel about sharing these? Most modelers just state in their ReadMes about credit, etc; I wouldn't want to step on any toes by doing what I did above, releasing the 3 ship version of a model I didn't make.
{edit} duh, I forgot, you could just always paste twice in step 1, you just have to remember to "select none" in the "Polygon" menu between pastings.