Puulis: Sorry for necro on a 6 year old thread, but this is one of the top google results for the issue and I found a definitive solution for this. Also the audio desync, and it applies to SR3 as well. At least for nVidia, but may be possible on AMD too.
Setting a framerate cap -- ANY cap, as long as it's not absurdly high -- in nVidia control panel solves all the issues SR3 and SR4 have. Even if you aren't hitting the cap before you hit your vsync target. For example, I run the game vsynced to 60fps, but setting a 150fps cap in NVCP totally resolves the issues even though the game never actually hits that framerate, and runs comfortably at the 60fps vsync target.
I suspect something under the hood on the CPU side of things is spinning to the moon and causing issues, and setting a hard framerate cap on the game prevents whatever it is on the CPU side running too fast for its own good.
Do note that cutscenes are hard capped to 30fps for animation keyframing reasons, but now they'll actually hit that target.
Thanks for necroing. I set a Radeon Chill limit in adrenaline and it also worked.