Only occurred for me on my Indexers (Splunk Enterprise).
Domain (Service) Account.
Splunk Domain (Service) Account has Full Control of the Splunk directory.
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Seconded.
Thus far though, I've only seen the error during our Indexer upgrades.
I didn't see the error during our Cluster Master, Deployment Server, Forwarder, or Search Head upgrades. I don't yet know whether there will be adverse effects.
Update: With 6.1.1 released, are you still seeing issues?
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