I personally have two suspicions that come to mind.
1) Is there frame skip enabled in the emulator? Frame skip is only supposed to occur when the computer can't keep up, skipping the rendering of frames as necessary to try to get the game running. However, I think in some cases, frame skip might activate even with a fast enough PC, so you might want to try setting it to 0 to see what happens.
2) Does the frame rate of the game you're playing mismatch the frame rate of your monitor? PAL SNES games run at 50 FPS, and NTSC SNES games run at 60 FPS. That means depending on which games you're playing, your monitor should also be running at 50 Hz or 60 Hz respectively. If it isn't, you might experience choppiness. For example, if your monitor runs at 75 Hz, than any SNES game will likely appear choppy to you. Using multiples of 50 or 60 should be fine, though. For example, if your monitor runs at 120 Hz, plaiyng NTSC games at 60 FPS should work just fine. In short, I recommend checking the refresh rate on your monitor and maybe switching it.
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