I've had that problem at eNom as well. In my case it was when I moved domains between different Magic Folders with different DNS records. The changes looked correct in the control panel, but they never took effect when resolving. I had to remove the domains from their Magic Folders and change them manually twice (once away from the correct servers and then back to the correct servers, and in between checking the whois changed). The whois didn't reflect what was in the eNom's Control Panel, until I finally got it corrected.