I had this problem with a setup of a site with Polylang and WP Job Manager – the post type for the jobs didn’t appear in the list of post types that I could decide whether to be translated or not.
Turns out WP Job Manager has a wpml-config.xml file in it’s root directory prepared for WPML compatibility. Polylang is playing smart so it’s looking for this kind of files and is interpretting them the same way as WPML would.
Editing the wpml-config.xml solved my problem, although it would be whiped by the update of the plugin. As a PoC it works and next step would be to try to override the settings through another plugin.