Help identify what uses the CPU when the Activity Monitor list of all processes does not help
Testing seems to show that the culprit is Intel's Turbo Boost technology, which disables processor cores on the fly without telling the OS.  Since they aren't running the CPU idle process, activity monitor doesn't account for them, and it appears that the machine is under 50% idle when the reality is that it's near 100% idle.

At the moment it doesn't appear as though this can be easily disabled or controlled under OS X: How can I disable CPU throttling and CPU disabling?

Turbo boost is built into many Core i7 and i5 processors, and some of the latest Core i3 processors.  You will have to check your processor version against intel's list of Turbo Boost capable processors to find out if yours has it.  If you don't have sandy bridge, you probably don't have turbo boost.