If I understand it right, there are 2 objectives for Commonwealth Rising. One to investigate the comm room or whatever, one to help Lupe with remote management. The latter does not complete when RM does, and this prevents the former from falling in place I guess. I don't remember the exact sequence but this happened to me when Remote Management was started during Commonwealth Rising (the call from Jake about it all going to shit lead to meeting him for starting Remote Management, instead of the big comm room meeting).