Vsync does not really work good in Nestopia. It should handle frequency differences in hardware, sync to monitor refresh. The game or sound would be slightly faster (or slower if you are using less then 60 Hz) but mostly unnoticeable with the effect that scrolling is totally fluid. Have a look at VirtuaNES - this emulator does it the right way and it works absolutely perfect!
There is a nice article about that on http://www.neogaf.com/forum/showthread.php?t=421792
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