Check the number of threads that you are running. They should be the double of the numbers of physical CPUs you have.
Open Nuke and press X, the script command windows will open, leave the default expression that is in there since it's the one you will use. This will return the number of threads you are running.
If they are half of what you have in terms of processors set the -m flag to the correct number to start nuke.
Also avoid using HT on, I personally have more problems with it in nuke then any speed improvements.