Custom Rig Mapping isn’t seeing all the bones

When using Attach Custom Skeleton to RRM3 the script doesn’t see all the bones in my custom bind skeleton.

I previously used Rapid Rig to generate addition face and hand bones, then I duplicated and moved these joints into my custom bind skeleton. I changed the names and moved them out of the Single Joint Hierarchy layer.

These new joints should be included in both the bind skeleton and the RRM controls so it’s not a matter of not matching the count or position.

Is there any special filtering or rules that limit which joints are added when map selected joints is chosen?