Are there more then one startpos files that use those unit- & buildprod files?
The problem could be that you didn't add the new faction(s) to the other startpos files.
You have to put DeclareFaction:: "Factionname" in all startpos files that use the same unit- & buildprod files. The DeclareFaction:: lines are somewhere at the top when opening the startpos files.

That's if I remembered the solution to the problem correctly.