After receiving the message to restart Logos, I got this:

Something similar happened with beta 1.
I've worked out it's BitDefender that's causing the trouble. It allows the upgrade to the next version, but then rolls it back later. I've submitted the .exe to BitDefender but because I think it's using heuristics rather than a signature, I'm not sure it will do any good. Perhaps you could reach out to them, or at least test it internally. I'm using BitDefender Total Security 2018, and it's the Threat Defense module that's causing the problems.