On Kyso disconnect your Github account: go to https://kyso.io/github, click on the Reauthorise dropdown and then click "Disconnect Github account".
Go to the Authorised OAuth Apps page in your Github settings: https://github.com/settings/applications, find the app called Kyso and Revote its access to Github.
Go back to Kyso and add your Github account again, on the Github Authorisation page make sure that your organisation is checked:
4. you should now see your Organisation repositories in the list.
If the organisations are not listed on the Github auth page, make sure that you are a member of that organisation and that third-party applications are allowed. If trouble persists contact us at firstname.lastname@example.org