Could you include what gets written to your syslog while the VPN
connection is established?

SIGUSR1 to dnsmasq tells you what server it's talking to, but
unfortunately not for what domain...

Based on your described symptoms, I'm suspecting that the openvpn plugin
told NM to configure dnsmasq only for the domains pushed by the VPN
server rather than for all domains (as it should when you route
everything over the VPN).

If that's what happened, you should see log lines like:
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.30#53 for 
domain stgraber.net
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.30#53 for 
domain 16.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.30#53 for 
domain 17.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.30#53 for 
domain 18.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.30#53 for 
domain 19.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.30#53 for 
domain 22.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.30#53 for 
domain 56.149.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.31#53 for 
domain stgraber.net
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.31#53 for 
domain 16.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.31#53 for 
domain 17.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.31#53 for 
domain 18.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.31#53 for 
domain 19.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.31#53 for 
domain 22.172.in-addr.arpa
Jul 18 22:14:06 castiana dnsmasq[9394]: using nameserver 172.16.20.31#53 for 
domain 56.149.in-addr.arpa


And resolution of any of record that's part of one of those domains would 
succeed.

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https://bugs.launchpad.net/bugs/1603898

Title:
  DNS resolution fails when using VPN and routing all traffic over it

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