If your Power Commander III is not communicating to the Control Center Software, the first thing to do is to make sure the USB connector is fully seated into the power commander. If there is any silver showing on the USB connector that plugs into the Power Commander, it is not completely plugged in. It is a tight snap-in fit.
The Power Commander also needs to be constantly powered in order to communicate fully with the computer. The green light on the face of the Power commander needs to be constantly on in order to communicate. Make sure you have a fresh (above 8.5 volts) 9-volt battery if using the battery adapter. If using the bike's power some bikes need to be running to provide the constant power needed rather than just turning on the key. Make sure you are using the latest software version available. If you need to check your software version, go to the "Help" menu in the software interface and select "About".