If you can't see your organization projects or have any problems regarding metrics (e.g. you don't see any issues and your pull requests aren't analyzed), please check if your user account has a duplicated copy of the project on the organization.
The ideal scenario for your organization projects is to have only one copy of it added to the Codacy organization, added by someone with write permissions on that repo.
In case you have a duplicated project on your account, please delete it and use only the one available in your organization.
In the unlikely event of not seeing projects for one/multiple organizations, please go to your GitHub settings and revoke Codacy OAuth application.
After revoking Codacy from the GitHub Authorized OAuth Apps, go back to Codacy and add a project to see the "Authorize Codacy" menu. (Note you may have to click "GitHub" on the sidebar to request for Codacy's permission on GitHub's side)
Click "Grant" on each organization, to see their projects on Codacy.