Are you using a USB cable for the Commercial Series? These suggestions are based on my experiences with a USB cable.
First, make sure you have the latest drivers for the Prolific 2303 chipset. They can be found at prolific.com if you need them. Anything else may cause problems.
Second, make sure the programming cable is plugged in and recognized by the computer before you run the Commercial Series CPS. You may have to go into the device manager and confirm this.
Third, I found with the Commercial Series CPS that you have to set the comm port every time you run it. Just fire it up, go to Edit ---> Preferences and set the Comm Port EVEN if it looks like it is already pointed at the proper one.