After updating to After Effects CS6 11.01 I started getting an error message about CUDA not working.
Strangely CUDA was still working fine in Premiere Pro CS6, so it had to be the AE Update.
And I am running the latest CUDA.
The thing is it just wasn’t showing up in After Effects and was using CPU instead of CPU for CUDA.
I tried trashing After Effects preferences, but that didn’t work, so I found and downloaded the standalone 11.01 update installer and that fixed the issue for now.