Hi James
The program/Certification progress prior to Totara version 12 was based on the completion of each courseset meaning that all courses in a course set had to be completed before progress was shown in the program.
In version 12 this was changed to take into account the program logic and individual course completion
From your screenshot it looks like there is a courseset that has been completed. I think including the AND between courseset means both these need to be completed before progress is registered.
To get around this then you could use a THEN between coursesets - this means the order is defined
regards