Thank you for your suggestion about the "CPU PLL" Setting. I used it to solve my related problem.
I have an Intel NUC D34010WYB where the same thing was happening: the USB devices did not work after the machine woke up from sleep including the mouse and keyboard.
I did not have the "CPU PLL" setting that you mentioned but I did have another setting under Performance called "CLOCK PLL" that I changed from "LC-PLL" to "SB-PLL" and that solved the problem. (Not sure why it fixes it but it did.)
I did not notice when I posted my note that this was the "Mountain Lion Desktop Support" forum. The problem I had was on a Haswell processor with El Capitan. I do not know if it would happen in Mountain Lion or even if Mountain Lion will run on a Haswell processor.