When you attempt to create an issue on GitHub, if repositories from any of your GitHub organizations are missing it's probably because at the time you authenticated with GitHub you didn't grant access to all of your organizations.
If you didn't click the Grant button at authentication time, on GitHub go to Settings > Applications and click the Authorized OAuth Apps tab. From there, click the CodeStream application. On the following page, click the Grant button next to any organizations that you'd like to be able to access from CodeStream.
In some instances, you'll see a Request button instead of Grant, which means that the owner of your GitHub organization will need to grant you access.