Oh, I'd be willing to bet he can hear something outside. My dog can tell when people walk by in front of our house, and he's not got a low enough window to see them... I think he can hear their footsteps or something, even when I'm sitting next to him and I can't. My guy (Sammy) has had similar problems sleeping through the night, and I posted about it recently and got some great advice (mostly about his crate likely being small for him) if you want to search that thread and read it. I have also seen Sammy be bothered in the house by wind he can hear outside- maybe wind at night is bothering your guy.
By the way, when is your little Berner coming?