I've been googling around to try and get awnsers to this myself, only to find that a number of people are having similar problems. And then remembered my work with DD-WRT and IPv6, so gave the following a try.
This is because if we override the zone here, we cannot access the email servers at the other end of the tunnel, but when we connect it changes our local search order. We do not have access to change the DNS zone at the other end.
It does not however, modify your DNS servers or connection order, so there is something you can do. Install DNSmasq. You can specify results for certain queries in the configuration file, for example:
You can also configure this on the same machine as your existing DNS server, simply set it to run on a different port, then set DNSmasq to forward any queries it cannot answer itself to it, either in resolv.conf or in the config file itself.
This can interfere with DNS registration, so be careful and creative with your solution if you still require it. You can also use DNSmasq as a DHCP server if necessary, but I do not have the access to disable the existing one here.