Dear alexrmz,
Welcome to Centrify Commmunity!
I believe this is a follow up question regarding to the existing support ticket you have filed with our Support team, therefore I will go ahead and file a new ticket for you regarding to the AD and FV password update issue.
However, base on our inital research. This appears to be a native OS X issue as you can find many others reporting the same problem:
https://jamfnation.jamfsoftware.com/discussion.htm
https://groups.google.com/forum/#!topic/macenterpr
https://discussions.apple.com/thread/4715315?start
According to the last link in the Apple thread, it looks like you'll need to remove the user from the FileVault list and then re-add him back in order to get the passwords to sync up again. As I will need to perform some more tests on the latest OS X 10.12 to ensure the behavior and see if Apple have fixed this issue, I will keep you posted with any update. Thank you!
Best regards,
Ivan Chan