Are you running the perfcollector local to the x64 server or remotely? I monitor all of my SQL Servers remotely using SQLH2 on a x86 server, and I get no problems collecting from my x64 servers. If you are doing local collection, try using a different server to collect the counters, or try it from your workstation if all you have is x64 servers. The server doing the collection is collecting for 28 total instances and has no trouble doing so.