From the README.txt in the directory of the program :
"GPU mining can be disabled by specifying the -S opencl:noauto option."
I can't say any more because i use cgminer......
With cgminer do you still have to specify each comm port?
Technically, no, but I still have not talked to anyone who has gotten the new version of CGMiner to work (the one that doesn't require you to specify each individual port). Most people I know still use 3.1.1 as it works better. It's not that big of a deal. You specify once in the config file and then you don't have to worry about it unless you change your HW setup.