First of all you should never use two coats of stain. With two coats of stain you are likely to let some of it dry on the surface. Then when you put a finish on it the finish adheres to the stain instead of the wood and later peals off. I suspect your shinny places are just that. I think the dull places are where the finish was able to soak into the wood. More coats would cure that but the rest of it is unknown if the finish would stay or not.