@rrmeines it shouldn’t (in theory) make a difference how the wysiwyg field is being inserted since the ‘acf/init’ hook fires after ACF is loaded, so wpautop should be removed for any fields that use it.
Maybe there is something else that is using the native ‘the_content’ filter which is overriding the acf filter?
I’ve never tried using wysiwyg in a repeater or flexible context though, so that might be related to the problem you’re having.
