I am part of multiple organisations on Github. This is my github profile. I tried syncing with Github today and faced a problem.
After authorising utopian with Github, many of my projects were not imported. In particular, none of the projects from an organisation (UprootLabs) were imported into utopian.
I did ensure that that organisation permission was given during the oAuth process. And I double checked this by going to my github settings.
I can't be sure this bug is reproducible for everyone, because their organisations would be different. But for me it is always reproducible. Even if I click "synch with Github" multiple times, the projects from that organisation are not imported.
I hope this gives enough information about the issue. If any more details are required, I will be happy to share.