I'm not seeing what you are seeing. I'm actually a bit confused by your workflow. Nevertheless 

Usually I don't use Create New Master for the creation of blank masters for INJ destination, which I won't bother explaining but

Here's Maya's Ball Joint Doll

I create 3 blank masters in the body (they can be renamed, at any time, in a few ways, including one way that's contrary to what it says in the manual...)

I export via Pmd Injection file pz2

The resulting file does not call on a pmd, there's no morph data of course, it's empty valueParms

I load a new instance of BJD and apply the INJ pz2... the 3 empty masters appear in the figure as named. If I had created 20 blanks and passed them on it would be the same. Not sure why you are needing to recreate them manually and name? Is this for conformers?