Why aren't repos from GitHub organizations listed?

When you connect to GitHub as part of creating an issue codemark, all of the repos you have access to should be available for selection. If repos from any of your organizations are missing, it's probably because at the time you authenticated with GitHub, you didn't grant access to all of your organizations.

GitHub Authentication

If you didn't click on that Grant button at authentication time, simply go to GitHub and navigate to Settings > Applications and click on the Authorized OAuth Apps tab. From there, click on 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.

GitHub OAuth Apps