Mark Kindy
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FWIW: While testing an unrelated issue on unrelated software, I had to disable Intel's SpeedStep technology in my BIOS (CPU kept throttling well below nominal speeds even under high-demand in this other program). Afterwards, when I noticed significant improvements in that program's performance, I ran MC on a hunch and am no longer experiencing this issue. I don't even know why SpeedStep was enabled by default on a desktop machine (not like it's on a battery, and electricity's only $0.10/kw-hr), and I certainly don't know why the CPU was not going full-throttle under heavy load, but it might be worth anyone else exploring on their own system.
If I can offer any insight, I am experiencing this problem and believe it to be related somehow to mouse movement. If I move the mouse quite slowly, there is no stuttering; but if I move it quickly, as I usually will, the stuttering is immense, making the game unplayable. This can also be demonstrated even on the start screen; the blurry background will stop rotating if you move the mouse in quick arcs and lines, and resume once the mouse pointer stops moving.
If this helps, here are details for my system:
Windows 8.1 Pro
Java 8 64-bit
nVidia GTX Titan
Cyborg MMO7 Mouse
All drivers up-to-date as of this post.
As mentioned above, it was resolved for me when I disabled "Intel SpeedStep Technology" in my BIOS. For some reason, my Core i7-4920k was not interpreting high demand from the game (or possibly from Java) as any reason to boost the clock to nominal speeds – it continued to operate as if the machine were idle. I do not have the details to know if this is something wrong with SpeedStep itself, with Java, or with the game.