Please make sure that the OAuth application on GitHub is granting permissions not only to your personal repositories but also to your organizational ones - to verify that go to your GitHub OAuth settings. Make sure that Zenodo is given access (green tick) to your organization under "Organization access".
After the change of any permissions on GitHub, you will have to synchronize this information with Zenodo - navigate to your Zenodo GitHub settings page and click the "Sync now" button at the top. Your organization's repositories should appear in the list of repositories.