Mac does not restart, shutsdown instead
Since you didn't list enough technical details about how file vault is set up (for instance if you have auto log in enabled or disabled, whether you are using institutional keys or just having one or more users storing the unlocking keys in the user accounts so that the recovery HD can unlock things) - I'll start with some steps to narrow down what might be happening.

First thing is to check if the machines are capable of restarting by storing the file vault key in RAM:

fdesetup supportsauthrestart


If that reports "false" then your hardware might not support restarts with FileVault 2 enabled. If it's true, does the system reboot if you ask for a controlled restart?

fdesetup authrestart


Also, if you're not comfortable with the fdesetup tool, you might want to review some of the helpful articles from Rich Trouton's blog. You'll want to start with an old article getting the basics covered if the current articles assume too much knowledge of how fdesetup works as dealing with file vault from the command line is a lot like the proverbial "sip of water from a fire hose" to many.