I think the flat rate system is horrible. You have to work so fast to make a living you make unneeded mistakes.
I am a hard worker, don't loaf, and like to work but the flat rate system (or the way the dealership I worked at handled it) caused me to give up what should have been a good career as a ASE master tech.
Favored techs get the higher hour non warranty work. (I am not interested in sucking up to anyone. Its just not my thing)
I have also seen many mistakes caused by the fast pace one must work at. Cams not torqued in sequence causing them to ruin the heads that the tech had to pay for out of his pocket. Car backed out of bay to quickly and hit another that the tech had to pay for just to name a couple.
Sorry for your trouble original poster. They should have better customer service at the least.