[i removed my previous comment]
So the pages are in the project explorer, but not visible in the module security tab? Weird!
Did you try restarting the modeler? Did that change anything?
If not: i would say this is a bug in the modeler and you better report it to Mendix.
I had the same issue, following the Rapid Developer Learning Path.
This worked for me on Studio Pro 8.18.3.
Open the missing page from the list and go to Properties tab.
Under Navigation, click on ... for Visible for property and select a module role.
It should now be visible in the list of pages for Page access.