For reasons beyond the scope of this post I have an environment where I have Windows 2003 R2 64 bit running but SQL Server 2005 running on 32 bit.
Having fired up perfmon I could not see the SQL Server 2005 counters which left me in a state of confusion. Having had a quick google I found a very good post from Tony Rogerson, this can be found here.
I had fired up the 64 bit version of perfmon so the 32-bit counters for SQL Server do not appear. To get around this you need to open the 32 bit version of Perfmon which you can do by running the following:
mmc /32 perfmon.msc
Having fired up this version of PerfMon all the SQL counters were available to me including the named instance counters listed under the name of the instance.