I was having some ipsec issues so i first suspected that the time may have been off.
To my surprise ntp.conf had no servers configured nor was ntpd running. But I had 3 servers in the VyOS config. I deleted and re-added the servers and then everything was as to be expected. Nothing unusual, maybe even the factory default:
del system ntp server '0.pool.ntp.org' del system ntp server '1.pool.ntp.org' del system ntp server '2.pool.ntp.org' commit set system ntp server '0.pool.ntp.org' set system ntp server '1.pool.ntp.org' set system ntp server '2.pool.ntp.org' commit