I recently applied for a mortgage with contrywide. My current mortgage broker just changed from wells fargo to countywide

I pulled my own credit before he did and my scores were very good. My 3 scores being 784, 823 and 854. I was told that the middle score would be used.
He came back to me with a middle score of 648. He said this is what his company recieved as my credit. After a week of arguing with him he said that mortgage companies basicly make up their own scores based on your credit history. I am 28, and have only ever missed one payment, one year ago with Nextel cell company. That is listed on my credit report and it is in dispute. That's it!! How can he change my credit score, is this even legal? Has anyone ever had this happen to them?
Please Help