Scammed by dealership??

Check out my situation and see if it makes any sense. A couple months ago, my check engine light came on and the car was running rough like it was lagging. I took it to the dealership where i got my car from and they tell me that I need an engine flush because deposits in the engine can cause the car to run roughly. Now I don't know anything about cars and i can't be without it, so i told them to go ahead with it. The thing is, it would cost about $530. About 2 days later, the check engine light came back on so i went back and b*tched at them about it so they checked the car for free. The guy tells me, it MIGHT be something with the sparkplug wires and that they reset the light and if it happens again to bring it back. In a span of 2 months the engine light would flash and then turn off. I didn't think that it was too serious of a problem and i need my car so I thought i'd wait until the light came on and stayed on. Which it did about 2 weeks ago, so I took it to another dealership and they said it was a coilpack problem. So they fixed it and the car's been running perfectly ever since.

I told the guy at the second dealership about what happened with the first dealership so he asked to see my invoice. He looked at it and said that they got the same misfire codes and that he didn't understand why they did an engine flush. So he printed out the misfire codes that he got and told me to talk to the people at the first dealership. The weird thing is, I looked at the invoice from the engine flush and the only thing i can see about misfire codes is that they found a total of 11. What should I do, i'm defimitely planning on going to the first dealership and talking to them about it, but I don't know how strong my case is and i'm confused about the misfire codes. Arrghhh, damn stealerships. Can anybody help me out here?? I'd appreciate it.