Jayco Eagle roof preblem

We have a 08 Jayco Eagle camper Van. Due to some slight damage to the side roof channelling,(resulting in a leak) we had the roof channeling replaced and a new ceiling installed (covered by insurance).I was very happy with the job. Ceiling appears to be better quality material. However, there is now 2 small indentations in the roof, either side of the center chanelling (each about half the size of a saucer). The water pools in the indents. The repairer advises that he dose not think he can do anything with this problem. He is currently working on it.

Has anyone had similar problems? Any advise appreciated.

Derek from Darwin