When adding a Source Repository of type GitHub, you're able to enter the credentials for a GitHub account and click Load Repositories to fetch the repo list from GitHub. However, if the account in question has more than 30 repos, only the newest 30 are shown in the Bamboo drop-down.

I'm guessing the cause is that the GitHub repo list API is paginated to 30-at-a-time, and Bamboo is only fetching the first page of results.