I'm pretty disappointed that this new, flashy computer may not be able to take advantage of the OpenGL capabilites of CS6 because of the brand of the GPU.
First of all, you are working with CC (version 12 of After Effects) - not CS6 (which was version 11).
Secondly, the only thing you're missing out on by not having an NVIDIA GPU is acceleration of the 3d ray-tracing renderer. That's it. And, since CC comes with a free (LIte) version of Cinema 4D, you have a superior option for creating 3d objects anyway. More info about the GPU in AE here. So don't worry about not having an NVIDIA GPU for After Effects. (Although, if you were really planning to use the 3d ray-tracing renderer a lot, I would have assumed you would at least have looked at the tech specs of After Effects before you made a big purchase.)
Anyway, to solve your problems, you will proably need to get rid of the CUDA driver that was installed. Luckily, since it's a new machine you haven't done much with it yet, if you're having trouble with that, you can wipe it and start over.
Thanks Szalam, appreciate the feedback. As you can tell, I'm not super-savvy when it comes to the under-the-hood workings of AE and GPUs. Definitely something I need to get familiar with.
I've submitted bug reports to Apple and Adobe, and I've explained the problem in greater detail to an Adobe engineer. In the meantime, I wiped the disk, re-installed Mavericks, and am now re-downloading all my Adobe goodness. Pain in the ***, yes ... but I'd rather have the peace of mind of a fresh start.