I had this same problem. For me this solution worked for SQL Server 2008 R2 Express.
SQLEXPRWT_x64_ENU.exe
(This is the name of the
file I used)/Action=install /SKIPRULES=PerfMonCounterNotCorruptedCheck
Of course this does not fix the underlying issue but it is a workaround because this fix also works on the principle of skipping the Performance counter check in the setup. The difference is this method worked for me when doing it through the command line failed.