Did sudo apt-get update then upgrade and reboot, My ADS-B says Im still running 3.1.0?
I've been having a somewhat similar issue.
I've got two Pi3b's co-located so I can compare antennas or other changes made to one system while keeping the other as a reference.
The two were installed a few months apart, but both using SD image 3.1.0.
I can't remember, but probably downloaded the image again for the second install.
The second Pi is behaving as you'd expect with the 3.3.0 upgrade (initiated from the Web control panel).
The first on the other hand goes through the motions and happily reports a successful upgrade until it restarts, then after a reboot, it reports 3.1.0 again.
It's not a big deal, but interesting all the same.
The main reason I haven't just loaded a clean install is that the local power is not particularly reliable and it's an easy way to know the power has been out even when I'm out of the country.