Well this is really weird.
I switched my theme to Twenty Fifteen and copied over my functions for the custom post type and the posts per page, and it’s still only displaying just 9 posts per page.
Right now I’m on my local setup, using MAMP and VirtualHost X. Could there be some sort of cache issue happening here? My apache server has been turned on and off a few times already, though, so I don’t feel like that could be it…
I suppose I’ll have to try putting a quick fresh install together like you did, and hope its just a weird glitch that I wrote into the theme somewhere that I can bypass on a fresh install.