I installed latest NPM and APM versions today only to find out my perfmon counters disappeared for Solarwinds and SQL on the host machine. After 2 hours of trying stuff I found a more detailed step by step tutorial and when using BSTI's comments at the bottom I rebuilt my counters. Hopefully this helps someone:
blogs.msdn.com/.../troubleshooting-sql-server-2005-2008-performance-counter-collection-problems.aspx