In case anyone is having the same issues I had; I was able to join the appliance to AD and could see the computer account there but I could not get our domain to populate in the permissions list which is the whole purpose of joining it to AD. The fix for us was to allow certificate regneration.'
Log into your Appliance web interface (https://servername:5480) > Admin > 'Toggle certificate setting.'
On the left hand side it should say:
Certificate regeneration enabled: | yes |
After that, reboot and watch the console, you'll see a bunch of messages about the appliance regenerating certificates. Once it came back up and i logged in via the vSphere client, our domain was in the list.