This was fairly well documented around the web but we're still getting calls on it so I thought I would post a quick heads-up in case you run into it. Basically the issue is that you start seeing alerts saying "Performance Module could not find a performance counter" in the OpsMgr console and for now the temporary workaround is to disable the rule. We're working on a fix and will post more information as it becomes available. Here's the original blog from the MOM Team:
If you are receiving alerts “Performance Module could not find a performance counter” in the Operations Manager Console, please perform the following steps to disable the rule via override...
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J.C. Hornbeck | Manageability Knowledge Engineer