Sorry for the slow response.
No I am not registering field groups via php.
The field groups are activated matching a selection of templates. The page is also a front page.
I am also using a combination of Repeater Field and Flexible Content.
The odd thing is that the frontend is showing a blank page, as if the logic goes:
Use field group that match template -> field group is in trash – exit
Or it matches the active field group and then finds one with same name in the trash.