So I just spent 3-4 hours hunting down what might possibly be the most counter-intuitive, bizzare, random, the-devil-must-have-incarnated-himself-as-a-bug, bug i have ever encountered.
Under certain bizzare circumstances, on a single-core laptop with a not so new graphics card, a blank screen would render at around 800 FPS, but the mouse itself, along with all of the windows GUI, would lag like crap. I was able to duplicate this effect on the open-source irrlicht engine. This effect goes away if image-based text is rendered on the screen or if an animated model is rendered. A normal model doesn't make the effect go away, regardless of whether or not the animated model is actually animated. I tested this phenomena with my graphics engine, and found that the effect appears to go away almost entirely when rendering thousands of particles. Therefore, my conclusion for this bug is as follows: If there aren't enough objects being rendered on the screen, the mouse lags.
The solution for the lag problem is, apparently, to render more stuff.
*throws himself off a cliff*