Many important networking and firewall settings are lost after a VPS reboot due to /etc/network/interfaces being overwritten by the hypervisor (KVM in my case, a "bare metal" hypervisor). I believe this is a known problem (or possibly a feature, intended to ensure communication with the server) and I understand why this would be difficult to avoid. In particular, on my VPS I find I lose dns-nameservers, the inet6 gateway, and all but the default inet6 address. Also the firewall is disabled because the iptables-restore line is lost.
The real problem comes when trying to fix those settings. In webmin 1.782 running on Ubuntu 14.04 LTS, the Networking > Network Configuration > Routing and Gateways configuration for inet6, the DNS servers setting and the Linux Firewall > Activate at boot setting seem to be accepted but they don't seem to "stick" or have any effect on /etc/network/interfaces. In other words after refreshing the screen they're back to their old values.
I did eventually manage to restore the settings from a webmin backup (although I didn't realise it for a while, because of an old bug where the restore operation reports "0 files changed" even though it has in fact been successful).
I'd rate this a "Major" problem because the loss of DNS resolution, inet6 connectivity and firewall functionality are potentially severe problems despite (perhaps also because) they are not immediately obvious.