I'm experiencing an issue using Unity 4.3.2 and standalone builds. If I turn on VSync in the project's Quality settings, running the game at the native monitor resolution, I'll frequently get high framerate spikes (over 100FPS), and a strong stutter for a few frames, and then it drops back down to 60FPS and runs normally. If I run the game at a lower resolution (800x600 for example), the framerate stays at around 500FPS and the stuttering is consistent.
However, if I turn off VSync in the Quality settings, and force it on in the Nvidia Control Panel, I don't experience any stuttering or framerate spikes, nor when I turn off VSync completely (but lots of screen tearing, which is very ugly and distracting).
Can anyone explain this behavior? Is there anything that can be done to circumvent it? I'd imagine other Unity developers have used the built in Unity VSync with success before (or maybe not?!) so I'm hoping I'm just doing something wrong on my end.