If you observe high CPU usage on systems running the Windows agent, try disabling unused counters (e.g. IIS, SQL, Exchange, etc.) and then restart the agent.  If this does not resolve the issue, there may be corrupt counters that need to be rebuilt.  This condition can also be detected by observing the following symptoms:

• Poll Agent is not returning all values.
• Event log errors related to the agent.
• Errors in the debug log file.

For more information, please refer to Rebuilding Windows Performance Counters.