There are either issues in vpnc when connecting to strongswan, or in strongswan itself. Configs that work fine with the built-in IPsec client in iOS and OS X, Shrewsoft, and others fail with vpnc where it should function the same as the others. My gut feel is it's a vpnc issue of some sort that racoon just didn't trigger for some reason, given all the other similar clients work fine in the same circumstance. There are a number of instances of people using vpnc with strongswan, though many of those date back quite some time. I updated the bug ticket and will revisit as soon as time permits (in the process of getting 2.2.3 to release this week).
https://redmine.pfsense.org/issues/4784