By default applying Latest service pack of OS should fix the corrupted perfmon counters.
Since you are at Windows Server 2008 R2, you don't have any Service packs available and hence you can try fixing it out in registry..
http://support.microsoft.c
Make sure you take a registry backup before doing these changes.
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by: Nobletucky2004Posted on 2009-10-30 at 09:23:25ID: 25704492
Windows Server 2007 R2, BizTalk 2009, SQL Server 2008, BizTalk LOB Adapter Pack 2.0. Post the installation of the Adapter pack the performance counters registry corrupted and we were unable to use the command line utility to rebuild the registry successfully. As a result all appication using any perf counter failed to load, MMC would not load.