I've seem to have found a solution for this. I don't have the slightest explanation, but it seems that adjusting the PC monitor refresh rate fixes this issue. For me, setting it to 59hz instead of 60hz fixes the problem (I don't have any other refresh rate options). Apparently, Nestopia does not like the 60hz... who knew?
Although I can't test anything lower than 59hz or higher than 60hz, I'm sure that other refresh rates will work just fine. This fix (for some) comes with a very minor cost: vsync feature in windowed mode will not work. However, it will still work in fullscreen mode.
I hope this discovery helps those who are having similar issues.
Notes: Tested with the latest unofficial Nestopia build at this time, it can be assumed that this fix works for the previous official builds.
Last edited by Samurai Fox; 03/23/11 05:24 AM.