It seems fiducial markers with id 0 are actively ignored in the mapping process. No blue line is drawn between existing markers and marker id 0, and /fiducial_map does not publish fiducial_id: 0
Replacing marker 0 with any other marker fixes the issue.
Fiducial id 0 had a special meaning in the past. In the kinetic-devel branch on github this meaning has been removed, so if you build from source it should work as expected.
It seems fiducial markers with id 0 are actively ignored in the mapping process. No blue line is drawn between existing markers and marker id 0, and /fiducial_map does not publish fiducial_id: 0
Replacing marker 0 with any other marker fixes the issue.