Seeing as nobody has answered this one here's one solution.
I experienced the same issue today. I resolved it by restarting the following services in the following order on the affected servers:-
Cisco RIS Data Collector
Cisco RTMT Reporter servlet
Cisco CallManager
Once restarted my RTMT session cleared an error message that stated 'RisDC service stopped to monitor the following counters :\\CM_IP\Cisco SIP(Trunk name)\CallsActive'
Hope this helps somebody..