I am running Ubuntu 16.10 on my laptop and I am sure it is not a serious problem. I just downloaded the gnome desktop package (with the lightdm manager) since unity wasn't my favorite. Even the login screen was fine. It booted well into both the unity and gnome desktops. There was a third(five in total) option called "gnome on Wayland". I logged in with this when I got stuck in a command line with no GUI. I don't know what they call it but we usually see it blink between the login and the desktop environment.
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