I've managed to solve this problem.
First, ipv6 was a red herring. I just got lucky that the ipv4's kept being assigned in the right order.
The real issue was that, when there are multiple VPNs, there is a little selection window that allows you to specify which VPNs the client specific override is assigned to. This determines which folder the config file is written to.
I found out the csc was written to the wrong location, because when making a second client override, the configuration will default to selecting the next server, not the one you selected last.