You are implying that you are using an external runtime linked to both P12 and P13, subsequently, they share content.  You have external binary targets turned off in your preferences.  BTW, external binary targets create the PMD files, so if you have it turned off, Poser will not create them by default.  So far, everything appears to be set up correctly.  I haven't come across that particular problem with P13 but I haven't created that many injection morphs in P13 either.

I would submit a ticket to the tech team about your issues.  You might provide them with a test sample.