To my knowledge perflib disables performance counters if it believes they have caused an issue like i.e. an ungraceful shutdown.
Do you have any information of what has caused the ungraceful shutdown? Was this a hardware failure or a power outage?
Have you checked the Windows event logs for any messages from perflib indicating what the reason might have been for disabling the counters?
According to this Microsoft TechNet article you can prevent perflib from disabling counters.