Comment 52 for bug 1624317

I can confirm this works for multiple vpn connections and after wakeup from system suspend on Ubuntu 17.04. I encourage you to install the patched .deb or follow the instructions to build it from source and see for yourself. I'm honestly so glad this fixes dns leaks for using openvpn through the network manager gui on Ubuntu that I'm switching my primary machine to 17.04. :)
Please let me know if this resolves your problems with DNS leaks using a vpn via the network manager.