I remember something like this from many years ago.
Do you notice the stutter if you look away from the screen and use your peripheral vision? I seem to recall that some people are more sensitive to it than others, and that it tended to disappear as scene complexity grew.
Also, are you sure your monitor is at 60hz? Many run at 59 *or* 60 (my Dell can be set to 29, 30, 59 or 60) - perhaps there is a hardware mismatch somewhere.
Yep, definitely happens if I look away and use peripheral. Didn't know that could happen though, that's cool. I will check now to ensure that the monitor is in fact at 60hz, but if it isn't then VSync should be able to figure that out I would hope. There is something with frames being dropped though, some way some how.