Quick update: E-Visa worked totally fine with Asiana at JFK.

If you check-in online, make sure you go to the counter at the gate because they won't let you board without a printed boarding card. At this time, they'll check your passport and visa.

For some reason, when we got to Vietnam, customs said my husband was all set by that I needed to "have my Visa checked again" and they sent me to the VOA counter. Luckily there was no line and the guy there looked at my Visa for a few seconds, shrugged and stamped it. Then I went back to the original agent who had told me not to wait in line again and she waved me through.