I've noticed this problem too. VSync simply doesn't seem to work that well in window mode, which is strange. You can try manually waiting for vsync with IDXGIOutput::WaitForVBlank and Present(0, 0), or by using DirectDraw vsync methods, though I'm not sure if it will make a difference.
Thanks for reply! I've just tried:
[source lang="cpp"]m_pOutput->WaitForVBlank();m_pSwapChain->Present( 0, 0 );[/source]
The same problem.