You say you get to the power position. Do you follow the common advice to show the ball to Center Field? If so, that may be the cause of your problem. You might want to try just showing the ball to 3B (palm facing away from your body).
At the power position, you might also want to have your elbow bent just 45 degrees (leaning back toward CF) rather than 90 degrees (vertical).
There's nothing necessarily wrong with a windmill throw (aka throwing over the top) as long as your arm goes up because your shoulders are tilted. In fact, that's how you throw a 12-6 curveball. However, if your elbow goes above the level of your shoulders, then that's a bad thing.