I was recently installing BizTalk Server 2010 and encountered an error that I had not seen before:
Error 5009 Registration of BAM performance counters failed
After a small amount of investigation it turn out to be a known issue where the performance counter registry has been damaged.
To fix this problem open a command prompt as administrator and run:
This will rebuild the performance counter registry, after which you should be able to successfully install BizTalk Server.