I just wanted to chime in and say that I am having the same problem. We were running SEP 11 MR5, and I upgraded 3 servers and my machine to SEP 12.1. After the upgrade all 4 machines come up when I log in with the "Detected risks" popup. The quarantine is empty, and no risks were really found. My servers only have the AV component, and my machine has all components. This would appear to be some problem with SEP 12.1 as far as I can tell.
I really don't want to shut off the notification option, if possible, because if there *were* to be some sort of problem, I'd like to know about it. It seems that shutting off the notification option is not the ideal thing to do for the best security.