For the error that you see in the event viewer, a quick search shows that it could be related to a permission issue accessing the relevant dll like here. Though it seems like your error message is not pointing to the dll that provides the performance counter for PI Server subsystem's performance counter, hence it doesn't really explain the error with the PI Server's performance counter. Do you see any errors reported in event viewer specific to pictrdll.dll (this is the dll for PI Server's performance counters).
You mentioned that you do not see the counters in the PI SMT plugin for building performance monitor points. Do you also not see these counters when you view the performance counters of the machine using Windows' native Performance Monitor utility? (quick way to open this is go to start -> run and type in "perfmon"). Is this happening for all the PI Server's subsystem (like pinetmgr and pimsgss)? or it is specific to pisnapss and piarchss?