This problem is a real pain and I’m yet to determine why this issue occurs because my understanding is SQL Server counters are automatically installed as part of SQL Server installation. Let’s pretend you have recently installed SQL Server 2008 R2 instance on one of our company server. After the installation you noticed that SQL Server 2008 counters are not installed as part of SQL Server 2008 installation.
Now if you ever encountered this problem with SQL Server installation then by using an elevated administrator command prompt perform the following steps to re-register sqlctr100.dll, and run the file sqlctr.ini located in the binn directory for the instance:
Now you can see the performance counter for that instance in PerfMon.