Recently an issue came up where an admin was upgrading their Windows 2003 Server OS from 32bit to 64bit but they wanted to keep their ASP.NET application as is and running under WOW. The issue they hit was with monitoring performance counters. While using perfmon they can see the counter data they could not get these to log to a logfile. The solution here is to change the perfmon service to run under WOW64 (x86) if you want to log counters from a WOW64 process.
The following script sets this all up:
sc \\servername config sysmonlog binPath=%systemroot%\syswow64\smlogsvc.exe
Credit for the solution goes to Chris St.Amand of the Microsoft.com Debugging team.