In category detail, the list of feed-specific taxonomies is empty for selected Store View while for Default or other Store Views the taxonomies are available.
Taxonomies are Store View dependent and Store Views are in turn related to languages. Thus, at the moment of clicking on the button Get Feeds and Taxonomies in Koongo → Export Profiles the connectors downloads all the taxonomies and all their language-specific variations from Koongo Server for all active languages in your Magento. Languages are then in turn set up as part of Store View configurations.
Subsequent to Get Feed and Taxonomies action you may decide to enable previously disabled or add new Website, Store or Store View with a new language. However, at this stage the new Taxonomy is not present in your Magento instance and this is the reason why the list in category detail is empty.