This is usually due to some of the details of Github’s authorizations for integrations. You can read about how we handle Github authentication and the permissions you grant us in this page.
In that article, it goes over installing the Github app and granting access to either all or the specific repository you want. Pay close attention to the troubleshooting section, which probably has the information you need to figure out how to get those missing repositories showing in our setup wizard.
Another thing to consider is if you have a large number of repositories (in the hundreds). Due to how fetching a list of repositories via Github’s API limits to the first 100 or so repositories, the repository you want to link may not be visible. You can try working around the limitation by archiving or deleting redundant repositories. If that’s not an option, please contact email@example.com and the repository can be set manually.