I recently came across a server that was throwing this error into its message log: ntpd_initres[2619]: ntpd returns a permission denied error! It would only appear about every five minutes on the server, and restarting ntpd didn’t correct the issue. I stopped ntpd entirely, but the error still appeared a few minutes later. After examining the running processes, I found that there was a lonely ntpd process that was running using a non-standard method.