Windows 8.1. IIS 8.5. SignalR versions:
I have not seen this behavior before. Are the 20,000/s "RegOpenKey/RegQueryKey" operations lasting from 2-3 minutes continuously? Are all of these operations accessing the "HKLM\System\CurrentControlSet\Services\SignalR\Performance" path?
SignalR is designed to stop further loading of performance counters after any performance counter fails to load.
Perhaps installing the SignalR performance counters will resolve your issue. This will create HKLM\System\CurrentControlSet\Services\SignalR\Performance.
You will have to ensure that your application pool runs under a user in the "Performance Monitor Users" group.