I'm definitely not knowledgeable in this area, but I often read that you should set the game's fps limit to match your monitor. You can't possibly see anything more than your monitor's refresh rate, so anything extra is supposed to be a waste. Also, it should exactly match your monitor's rate. If the game tries to use too many frames or too little frames, it can cause a choppy appearance. Too little makes the monitor fill in fake duplicate data. Too many can cause this visual affect called "tearing", where you have a mix of frames showing at the same time. (Such as the clouds are from a different frame than the ground, and the trees will seem broken in half. Since this happens so quickly it might look choppy.)
So I would suggest looking up your monitor refresh rate (Hz) and going into the Minecraft options / settings page and setting the frame rate to match it exactly.
I would also try turning Vsync back on, as this is supposed to do the same thing, but with a different approach (Vsync limits sort of a frame caching system, which should achieve the same thing, but sometimes can still get tearing if things get timed right and I believe it's suggested you turn off Vsync if your fps are less than your monitor refresh rate... because that gets choppy too, or something? Not sure I'm understanding it correctly)
However, I'm only suggesting you try this out of desperation. Since you said turning v-sync on and off didn't seem to help, I'm inclined to think it's something else going on. To help you cope while you try to figure it out, try other things. Personally, I notice my game gets a bit choppy with these issues:
- starting the game in a busy areas (goes away after a moment of waiting and initial walkaround once everything's loaded) (large house in a jungle)
- using detailed texture packs (changing the most commonly seen blocks, such as dirt, grass, leaves, water, to smaller pixel sizes fixed it)
- if my security software is performing backgrounds scans or updates, or if Windows is downloading updates
None of those are probably a problem for you though, since you said you're getting 300+ fps, but it's all I can suggest. Hopefully a more knowledgeable person will come along.
