I don't think you have any other choice. I would. Was this all done through the Service Manager or just one of the advisors? Usually the Service manager is the one who will handle any and all warranty work. If he is the one telling you that you have to pay then go directly to KIA customer service at the numbers provided. I doubt the General Manager will be willing to help if the service manager is not helping you out.Think that will help?
On a side note. I picked up my SX 6 speed manual a week ago and I have no grinding from any gear at all.