It turns out we also had an issue with their website, which only applied $13 out of a $269 credit towards our upcoming trip. While it did take over an hour to resolve today, the phone reps were helpful, and never once implied I may have screwed up.

My self inflicted worry is that we have a 38 minute connection in JFK, which could cost us a day for a missed connection. But, the fare differential was $250 for the 2 of us (one way), so it's a risk we're willing to accept.