This can happen when App Center doesn't have permission granted to your GitHub organization. By default, the access is granted to personal repository only, not including organization repository. When you initially set up the access to GitHub, you probably have missed it.
Here's how you can fix the issue.
Step1) Please revoke the OAuth access granted to App Center in GitHub.
Step2) Go back to the App Center portal. It will show you the reconnect flow to your GitHub repository. Click Reconnect. This will redirect you to the initial OAuth setup.
Step3) As you can see, the access to GitHub organization is not granted by default. Click Grant to include GitHub organization repository.
Step4) You're all set! Now, you can see both personal and organizational repository. :)
If you have any question or trouble setting up the permission, please don't hesitate to reach out to our support team. You can reach out to us via the blue chat bubble in the App Center portal.