I used a configuration profile to require FV2, and to create an individual recovery key. When I scoped it to my test Mac the config profile did its thing and it encrypted the drive using FV2. I watched it finish, I rebooted and had to log in through the FV screen, as expected. So it's definitely encrypted. Verified by the FileVault tab on the target Mac, which says "FIlevault is turned on for the disk Macintosh HD".
If I look at that Mac in the JSS, under FV status it says 0/2, meaning the JSS doesn't think either of the partitions are encrypted (regular partition + recovery partition). And it shows up in my smart group that looks for FileVault 2 status is Not Encrypted.
What am I missing?
Test Mac is a Macbook Air, running 10.11.3, JSS 9.82