EDIT: I have resolved my problem by downgrading PHP from 7 to 5.6, this is not a great solution since Magento 2 should work fine on PHP 7, but for now it is an adequate solution for me.
I have just installed Magento ver. 2.1.3 on a clean debian install, no extensions or anything other than the requirements for Magento installed yet.
Whenever I try to create configurations for a configurable product they do get created successfully but after saving the product they disappear from the product configurations tab. The configurations do show up in the backend catalog, but they don't seem to be associated to the configurable product anymore.