Roots Discourse

Sage 9 and WPML string translation only looking in /resources/**/*.php for strings

We’re using sage 9 for a lot of our projects and recently we are having problems with WPML string translation only finding strings below the /resources/ folder.
It seems logical that it would do that because sage tells wordpress to look there for theme files.
But until some time ago (it’s hard to tell when exactly because not all of our projects involve WPML and existing projects not often add strings. I could verify i updated a string in early september) it worked flawlessly in every php file (app/Controllers, a custom namespace in a top-level folder) but now we can’t add new strings outside /resources/.
We’re currently using wpml 4.3.3 and string translation 3.0.3.

Does anyone else have this problem when using sage with the latest WPML?