Right, that will fix your issue, however, you're not really supposed to edit the conf files. You are supposed to append them through .local files. The issue is, I don't know how to append and remove something from the conf via a local file. I know how to replace it with something else. I'll give it some more thought.
This is the newest beta version of fail2ban and ipv6 is the newest feature. I guess this is one of the bugs they will have to fix.