We were not able to reproduce this issue on our setup . The steps I had followed was to make sure that both the controllers were pointing to the same NTP server and the error message was no longer shown.
The dashboard takes about 5 mins to refresh.Could you reconfigure the controller again to point the same NTP server and refresh the controller tab on SM2.0 to see if the dashboard is reflecting the changes.
I also had the same problem. I had the same information in options timed but one server was in upper case and the other lower case. I changed the server name to have matched case and the error went away. It was either the case issue or the system just hadn't updated yet from when a second NTP was added to one of the filers so they both matched.