Currently, you cannot install the GitHub plugin for repositories that you have access to through private organization membership, because our repository import can only read public organization memberships.
Requesting the scope read:org sounds like it will fix this. http://developer.github.com/v3/oauth/#scopes
HEY YOU Once we do something like this, we need to ensure private repositories do not get loaded into Bountysource and exposed publicly. That would not be good.