Quickly regarding instances:
Since AE is entirely 32-bit, it can’t access all of your cores without doing some trickery. When you enable multiprocessing, AE essentially sets up a mini render farm on your computer (this is where the trickery comes in). AE will start several “copies” of itself on your computer, and distribute the rendering job across each “copy.” For instance, when you enable multiprocessing on a Mac, you will see instances (“copies”) of a program called AEselfLink start up in Activity Monitor (which is the Apple version of Task Manager, of sorts). I believe on a PC, you simply see more than one instance of After Effects in Task Manager. There should be one instance launched per core of your CPU. In your case, the computer may be starting one instance per real core, or one instance per virtual core, hence why I asked.
Again, this whole process of getting AE to address all of your cores is a somewhat-sloppy-somewhat-clean work-around to non-native 64-bit support. Most of the time, it works great, but it can sometimes confuse itself over what cores/instances should render what frames (which may be the problem in your case). I would recommend checking with Adobe before anyone else, as it is probably a software and not a hardware issue (no offense to Adobe or their employees).
Hope this helps, and keep us posted!
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