Tried to debug my engine with VS graphics debugger and see that debugger`s frametime is the same as in my engine.
Just so I am sure that I understand, do you see the stuttering still in this frame time still?
Tried with nvidia GT 530 with vsync on. Stuttering has gone, but only with vsync = on. SO, I think this is likely related to some hardware problems.
This would not indicate to me that there is a hardware problem. Vsync essentially just forces your application to present at a fixed time interval, which is *precisely* what Buckeye suggested above. So there is likely something in your application that is causing a variable frame time, and you have to track it down. Start by isolating part of your application. Make a list of the things that are done every frame, and start commenting them out while taking measurements from the VS graphics debugger to see when it becomes smooth.
Once you have identified what the source of the stuttering is, then you can move on determine if this is something that can be fixed, or if it is inherently something that must be present. In the worst case, you can simply enable Vsync and forget about the issue, but this is a great opportunity to learn more about how your application is working - take advantage of it!