For anybody who runs into the issue of having two windows open, and runs across this question. Here is how I stumbled upon a solution.
The reason the code in this question is producing two windows is because
Frame.__init__(self, parent)
is being run before
self.root = Tk()
The simple fix is to run Tk() before running Frame.__init_()
self.root = Tk()
Frame.__init__(self, parent)
Why that is the case, I'm not entirely sure.