I am not an expert with virtualized performance counters and the use of rr. I just doubt if there will be any sort of restriction with Kaby Lake. But just a thought...
Have you tried to create a NEW virtual machine on the Kaby Lake host and see whether the virtualized counters work with rr?
For the Windows VM that I have shuffled around between host machines, if "Show Hidden Devices" is used on Device Manager of the VM , the Processors will show the Processors greyed out from the previous host. So it might be the case that your VM's virtualized performance counters are still looking for the old virtual processors that no longer exists and hence not wanting to boot up.