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In general, a given rendering setting in X-Plane will impact *either* the CPU or the GPU (i.e., the graphics card). Your overall framerate will be limited by whichever of those two is most heavily loaded.
In the ideal case, your rendering settings would be perfectly tuned to keep both your CPU and GPU fully loaded at whatever frame rate target you're trying to hit (often 30 frames per second).
But, if one component is overloaded---for instance, if the CPU-affecting settings are turned up much higher than the GPU-affecting settings---that component will become the limiting factor; it will "bottleneck" the rest of the system. In this case---with the CPU bottlenecking the framerate---you could swap in a hypothetical infinitely powerful graphics card and see little to no performance improvement... because it wasn't the GPU that was limiting your framerate in the first place.
So, my recommendation would be: check and make sure you're not bottlenecked on your CPU. The rendering options portions of the manual should give you an indication of which settings affect the CPU versus GPU. Likewise, the section on tuning the rendering options for best performance may be of use---it will walk through turning down all the rendering options to start with, then slowly turning things up until you find the best setting for your machine.
Do let me know if that isn't clear! :)
It might be worth posting a new question for this, but my first troubleshooting step would be to ensure other applications run as well as expected. For instance, you mentioned benchmarks---does Furmark (an OpenGL graphics benchmark) run as well on your machine as on other machines with the same graphics card? (Furmark is of particular interest, because it's the only benchmark I know of that uses OpenGL, the graphics library used by X-Plane, rather than DirectX.)
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