Sounds like he's a bit spooked by the night noises or lack thereof. I put mine to bed in their run most nights, not all, so that if we stay away overnight they can stay out and are used to it.
People are surprised at how much they love their run at night, although by 6:30am you can hear them in their rumbling in there and they want out
He may settle with age too. Make sure there is nothing out there that casts shadows, or that you don't move things round too much.
One night we came out to the setters huge bark and narrowed it down to the fact that I'd moved a large pot plant and it spooked her.