I've just installed a free version of GitKraken and logged myself on github. The software is working but when I pull a branch, I've always a red warning popup telling me "fetching pull requests failed"
Have you ever experienced that? Did I miss something in the configuration?
PS: my repositories are private
GitKraken can definitely work with private repos, but it would need to be authorized. Would you be able to login to GitHub using an account that can manage the organization, then click on the organization, then click 'settings' at the top, then 'third party access' on the left? Then you can either remove restrictions at the top to allow all third party apps approved by users, or click on the requested apps in the middle, then click on 'GitKraken', and select 'Grant Access'.
If the issue persists, would you be able to try logging out and then back in? You can click the button in the upper right and select 'login to another account' then login again. Then when you login using your GitHub credentials to configure the authentication again.