gummybear, can you please post the contents of both your Nestopia.log and Nestopia.xml files?
1. Launch Nestopia
2. run the game and wait for the problem to happen some
3. close Nestopia
4. Go to the directory where you ran Nestopia.exe from
5. copy and paste the file contents to this thread.
I am still suspicious that this may have something to do with the PC's hardware timer. Nestopia consults the hardware timer to determine if it needs to skip frames (to catch up to the actual time it should be at) or wait (to slow down to the actual time it should be at) to keep the emulation running at the right speed.
Nestopia can use an HPET if available, but then falls back on a multimedia timer. Or, if you are running with VSYNC enabled and "synchornize to refresh rate" checked AND your monitor refresh rate matches the ROMs framerate, it will just rely on Direct3D's built-in VBlank waiting (which is implemented via a multimedia timer anyway) to throttle the emulation.