Does your join table contain any records? When setting up a join table after the fact it will be empty of records. They need to be created to appear on the portal.
Perhaps examining this demo file will help sort this out for you: https://www.dropbox.com/s/oyir7cs0yxmbn6i/ManyToManywDemoWExtras.fp7
I suspect that this statement reveals the issue:
I have an author table which contains contact information, biographical summary, and a list of the publications each author has written.
That list needs to be replaced by records in your join table, one such record for each publication that the author has written.