Sql-server – SQL 2008 Server agent cant see perfmon counters

This doesn't exactly answer your question, but Paul Randal included a very helpful query for aggregating wait stats with one of his surveys last December. I have shamelessly copied and pasted it here, but am providing a link to his site, because there is a wealth of knowledge to be had from it. Wait Stats

WITH Waits AS
    (SELECT
        wait_type,
        wait_time_ms / 1000.0 AS WaitS,
        (wait_time_ms - signal_wait_time_ms) / 1000.0 AS ResourceS,
        signal_wait_time_ms / 1000.0 AS SignalS,
        waiting_tasks_count AS WaitCount,
        100.0 * wait_time_ms / SUM (wait_time_ms) OVER() AS Percentage,
        ROW_NUMBER() OVER(ORDER BY wait_time_ms DESC) AS RowNum
    FROM sys.dm_os_wait_stats
    WHERE wait_type NOT IN (
        'CLR_SEMAPHORE', 'LAZYWRITER_SLEEP', 'RESOURCE_QUEUE', 'SLEEP_TASK',
        'SLEEP_SYSTEMTASK', 'SQLTRACE_BUFFER_FLUSH', 'WAITFOR', 'LOGMGR_QUEUE',
        'CHECKPOINT_QUEUE', 'REQUEST_FOR_DEADLOCK_SEARCH', 'XE_TIMER_EVENT', 'BROKER_TO_FLUSH',
        'BROKER_TASK_STOP', 'CLR_MANUAL_EVENT', 'CLR_AUTO_EVENT', 'DISPATCHER_QUEUE_SEMAPHORE',
        'FT_IFTS_SCHEDULER_IDLE_WAIT', 'XE_DISPATCHER_WAIT', 'XE_DISPATCHER_JOIN', 'BROKER_EVENTHANDLER',
        'TRACEWRITE', 'FT_IFTSHC_MUTEX', 'SQLTRACE_INCREMENTAL_FLUSH_SLEEP',
        'BROKER_RECEIVE_WAITFOR', 'ONDEMAND_TASK_QUEUE', 'DBMIRROR_EVENTS_QUEUE',
        'DBMIRRORING_CMD', 'BROKER_TRANSMITTER', 'SQLTRACE_WAIT_ENTRIES',
        'SLEEP_BPOOL_FLUSH', 'SQLTRACE_LOCK')
    )
SELECT
    W1.wait_type AS WaitType,
    CAST (W1.WaitS AS DECIMAL(14, 2)) AS Wait_S,
    CAST (W1.ResourceS AS DECIMAL(14, 2)) AS Resource_S,
    CAST (W1.SignalS AS DECIMAL(14, 2)) AS Signal_S,
    W1.WaitCount AS WaitCount,
    CAST (W1.Percentage AS DECIMAL(4, 2)) AS Percentage,
    CAST ((W1.WaitS / W1.WaitCount) AS DECIMAL (14, 4)) AS AvgWait_S,
    CAST ((W1.ResourceS / W1.WaitCount) AS DECIMAL (14, 4)) AS AvgRes_S,
    CAST ((W1.SignalS / W1.WaitCount) AS DECIMAL (14, 4)) AS AvgSig_S
FROM Waits AS W1
    INNER JOIN Waits AS W2 ON W2.RowNum <= W1.RowNum
GROUP BY W1.RowNum, W1.wait_type, W1.WaitS, W1.ResourceS, W1.SignalS, W1.WaitCount, W1.Percentage
HAVING SUM (W2.Percentage) - W1.Percentage < 95; -- percentage threshold
GO

Have a try with lodctr /R, it will rebuild all performance counters from informations stored in registry.