First off stop analyzing every little thing she does. It's more control on your part. Understand that she's a grown up and is going to do what she wants.
Second, based off of your history, it's easy to see why she keeps believing you are controlling. You've pretty much gone off and done what you've wanted to (even negative) and she's had no say in changing your mind. What you're doing is more of the same.
By acknowledging her thoughts, you are doing just that - acknowledging how she feels. You say that you understand why she feels the way she does based on your history and you validate her feelings. It's not 'agreeing' to her decisions, just that she has a right to feel how she's feeling.
It's also why she gets P.O.'d that you don't call back right away. It's you being more controlling in terms of you doing things when YOU feel like doing it.
In the past it was like you didn't give a damn about what she or anyone else felt. Well now you're suffering the consequences. Tell her something like "you know, I've been doing some thinking and you're right. I have been lazy in the past and controlling. For that I deeply apologize for all the hurt it's caused." Or something like that.
Keep it short and sweet.
M-43 W-40 2D - 9 and 5
Emotion, yet peace. Ignorance, yet knowledge. Passion, yet serenity. Chaos, yet harmony. Death, yet a new life.