I have the same problem with the existing pages. We also have a three-item footer on the home page. However, when we attempt to update the footer module from the Home Page and check Display Module on all pages' checkbox, then select the update control and wait until the system is returned. The selected footer module is not copied to any other pages originally and currently without this footer entry.
We have upgraded DNN from 5.x.x all the way to 9.6.2, currently. The system operates on Azure.
a. How can this be corrected? (I have re-indexed the entire site)
b. Where in the database is the information displayed in the Added To Pages section of the HTML Settings panels?
c. Is this a known bug, i.e. deciding after page initiation have the system copy an HTML Module to all pages?