While I'm not familiar with the overclocking utility you're using, if I had to guess, I'd say the salient difference between X-Plane and other programs you've tested with is that X-Plane uses OpenGL for graphics drawing, whereas most games/sims under Windows use DirectX. My suspicion is that the overclocking tool doesn't work with OpenGL applications. (You could test this by trying it with another OpenGL application like FurMark.)
(As an aside, it seems weird to me that the GPU's clock speed is tied to the application running, rather than being set-and-forget at the operating system level, but maybe that's because I'm getting old? I admit I haven't fiddled with overclocking for the better part of 5 years.)