This is a weird one which has been happening for weeks and have struggled to get to the bottom of it.
We have had around 10 machines so far that have had issues with their User account not showing at the Login Window. These are local accounts (No AD) that have had Filevault enabled via a policy on the JSS. The user account will show up at the EFI login Window but a second Login Window appears and the account is not there.
Logging in with an Admin account the user is still present in the Users & System Preference and the home folder is there there.
Most of the users that have had this issue have been working on their machines for weeks without issues. No updates have been installed on the machines, no new config profiles, policies have been pushed at the time of the issue.
Hopefully someone may have seen this and can help
