Why aren't PRs/issues from all GitHub organizations listed?

When you connect to GitHub you should see all of your open pull requests in the Pull Requests section of the CodeStream pane, as well as all issues assigned to you in the Issues section. If pull requests or issues 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.

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. Note that 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 access.

GitHub OAuth Apps