Has there been any progress on this in the last month??
I thought I was going crazy. I have been working on a few big projects and then a while back I started getting jerking. I have been running circles trying to figure out whats wrong... when I started making smaller, very simple games (like here is a red square, move it around the screen with 8 direction behavior) I still get jerks every few seconds. Its just like the op described. Smooth, smooth, jerky, jerk, smooth...etc. The debugger still reports 60 fps at all times!
It has been a debug nightmare (except I did find a few bugs in my game that caused 1 frame lags, but nothing serious).