I'm running Qubes 3.2 (R3.2)
From Dom0:
$ qubes-pref
clockvm : sys-net
default-fw-netvm : sys-net
default-kernel : 4.4.38-11
default-netvm : sys-firewall
$ qvm-sync-clock --verbose
--> Waiting for network for ClockVM.
Time sync failed! - Exiting
$ timedatectl status
Failed to query server: Input/output error
any special firewall settings on the sys-net vm? What about the router or gateway connection?