I'm a firm believer in 'do it yourself'. All roof screws should have a rubber-under-metal washer. Those seal incredibly well. A dab of silicone in the hole wouldn't hurt . I'd check what they have done and see if anything obvious presents itself. If you don't find an obvious water entry point, don't go redoing their work.. I'd bet with a little investigation on the roof you'll find their oversight. If it's simple, fix it and move on. If not, I'd ask him nicely once more.. then sic the insurance company on him.