Allow Minecraft to Use More CPU

(Unmodded) Minecraft isn't multithreaded, so splitting it across multiple CPUs is not possible. However, I am not sure about a mod to allow for this possibility. There might be other factors you are ruling out.

From what I have found the mod, OptiFine, is supposed to split the load across two cores. (Otherwise, Minecraft only uses one)

OptiFine 1.2.4 Mod adds a lot of options for better looks and performance. Doubling the FPS is common. Moves fog away, adds mipmaps, chunk loading control (mod CAF), Smooth FPS, brightness control, VSync and many other.

Screenshot of Optifine below: