MacOS – Rebooting machine with macOS Sierra takes very long time

Since I upgraded my Retina MacBook Pro with macOS Sierra GM (16A319), rebooting the computer takes 20-30 minutes. I select Restart… from the apple menu, everything logs out, then the Mac hangs on a black screen for the rest of the time. I even have a mouse cursor. After a while it reboots normally, and booting takes 10-15 seconds as usual. If I force shut down, I can boot normally (except for the warning, that the computer was not shutted down properly).

I've tried selecting Boot disk in System preferences, change the boot disk from terminal, but it seems the problems is with the shut down operation.

I have only TripMode's kernel extension beside Apple's own modules.