Dealing with poor service

[Joe Henderson]

This might be answered on another forum but I trust the good advice here most always and need some guidance, 

After buying the property at auction we have started the renovation. One of the first items was the roof. The house in a Mid Century Modern modified A-Frame with a flat roof of about 1000 square feet. To make it short- we hired a local roofing company with about 1000 all positive reviews. Their bid was competitive and we were pleased with the way they came across. All of the companies would use the GAF Liberty product except one that would have torched down a roof. About 2 months ago they installed the roof and we were pleased about most of it with a couple items that were cosmetic that need attention. It has been an historic drought here in Georgia and the first time it rained was 2 weeks ago. We had multiple leaks during the heavy rain. After over a week we finally got someone to come out and have a look. There were a couple of areas with some ponding. He said that could be an issue and would get with the owner. After a week of more rain and leaks and a couple calls I finally got the owner to come out. Long story short he said the GAF product was not for flat roofs and should never have been put down. He has suggested putting down a silicone coating called GacoRoof that is for under water use.

I have reservations about them doing anything else since we have so many issues with not on their poor work but also the unresponsiveness I think they have shown. It's the first time I have ever had an issue with the way a service has been provided and not sure if I have any other option that to let them try and fix the issue with something other that a new roof. I mean they sold us on a product they should have known would not preform well- how can I trust them? I would prefer to get another company to lay down something better like EPDM. They have not been paid for any of the services yet BTW. What would you all suggest? Do I have any viable options other that letting them cover a new roof with ugly gray silicone?