I seem to recall something happening like this some time ago. However, if i recall correctly, I think the issue was solved in an update not by a setting somewhere. Since Fedora 27 stopped getting support on November 30 2018 I would highly suggest moving to F29 or F30 when you can so you will keep getting bug fixes and security updates.
Well, this was happening to me too in some past version. BTW I don’t remember, but some update solved the issue.
What you can do is looking at the logs: Viewing logs in Fedora :: Fedora Docs
And you could also test if the same issue happens with another user.
I tried rebooting from the menu (on a freshly booted system) with journalctl -f running. It did not reboot. No unusual messages. I waited a good 5 minutes and saw other normal log entries appear for systemd services, dnf makecache, cron tasks, etc. It simply did nothing until I tried a second time, at which point it rebooted immediately, as expected.
Ok I tried it: session-mate-save --logout and mate-session-save --logout-dialog both needed to be invoked twice to take effect.
The two attempts are required on each new login, not necessarily just on each new reboot. I did not stay logged in long enough to see if the issue exists on a new user login on a non-freshly-booted system. Something to try another time.
I also tried creating a new user, but logging in as that user resulted in a black screen with just a mouse cursor. Not sure what needs to be configured for the user’s graphical account to work.
Then it’s likely some config file in your user profile that causes the issue.
Perhaps strace can help you to localize it.
You can also try to use the exclusion method, but it may result in a lot of work.
What might cause this ignoring of only the first attempt to logout/reboot, and only for some duration of time after login/reboot? As noted before, after the system has been up for some time, login/reboot works from the menu on the first try.