I've had this problem before and usually it just resolves itself but we got a new macbook pro 2016 model with Sierra.
Mac is on the domain, I'm logged as the domain user which as an admin and user has a certificate assigned. User is the owner of that mac yet the encryption is not kicking. As you can see everything looks good except on the Disk Encryption Tab, it says No to System disk should be encrypted and I don't know why. It's only on this mac. Rest of the macs we have say Yes there and they're encryption just fine. On the server side, under the computer Inventory tab, there is no user showing as logged, however under the Users tab, the user who owns the machine is listed.
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