PerfMon Counters missing

In order to rebuild the performance monitors you have to run

lodctr /r (in your command line)

More details here

This behavior may occur if certain extensible counters corrupt the registry, or if some Windows Management Instrumentation (WMI)-based programs modify the registry.

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Rebuild the base performance counters Extensible counter information is stored in both of the following locations:

• The following registry subkey: HKEY_LOCAL_MACHINESoftwareMicrosoftWindows NTCurrent VersionPerflib09
• The %Systemroot%System32Perfc009.dat file and the %Systemroot%System32Perfh009.dat file To rebuild the base performance counter libraries manually, follow these steps:
  1. Expand the Perfc009.dat file and the Perfh009.dat file. These files are located on the Windows Installation Disc. The compressed files are found at DriveLetter:i386perfc009.da_ and at DriveLetter:i386perfh009.da_. Replace the files that are in the %Systemroot%System32 folder.
  2. Start Registry Editor, and then locate the following key in the registry: HKEY_LOCAL_MACHINESoftwareMicrosoftWindows NTCurrentVersionPerflib
  3. In the registry, change the LastCounter value to 1846 (decimal), and change the LastHelp value to 1847 (decimal).
  4. Locate the following registry key to search for services that have a Performance subkey: HKEY_LOCAL_MACHINESystemCurrentControlSetServices
  5. Remove the following values from the Performance subkey (if they exist):
• FirstCounter
• FirstHelp
• LastCounter
• LastHelp

From here