I tried different Merx/Kirby/Composer installations and never run into any issues, but maybe I am missing something.
Theoretically I can imagine that there might be some hiccups when you install Kirby without Composer and Merx with Composer (or the other way around). Could you please try to install Kirby and Merx with Composer or, alternately, remove composer and download the code from the release pages (Kirby/Merx).
I also tested installation via git submodule, wich also works without any issues.