Dogs know. That's really the bottom line here. Mine did something similar years back, just planted herself at the door and refused, shaking, wouldn't budge no matter what. Never found an explanation for it either.
The roof thing is interesting though - what kind of sound exactly? Heavy and slow or more skittery and fast? Because those are two very different things in my book. Round here in New Orleans we get possums and the occasional raccoon on rooftops and they sound surprisingly loud for their size. But an animal spooked dog for that long suggests whatever it was hadn't fully gone away, or left something behind that you couldn't detect but she could.
How long did the sounds last and did you notice anything the next morning - marks, displaced tiles, anything like that? Would help narrow it down. Not saying it's definitely something strange but the dog's reaction is the part that sticks with me. They dont hold onto fear without reason.