Blimey, that would have freaked me out no end. Dogs reacting like that is what always gets me, they pick up on things we just cant.
Had something similar years ago, not on the roof but in the garden, my old lab went absolutely mental at 3am barking at nothing I could see. Never did figure out what it was.
What sort of sound was it - like heavy footsteps or more of a scrabbling? And how big is your roof roughly? I always think the size of the area matters when you're trying to rule out the obvious stuff like foxes or birds. Would love to hear more detail on this one.