Commander Pro not working

I just recently bought a few new fans for my pc to replace a few chassis fans. Just before plugging them in my commander pro, I only had 3 fans hooked up to it. After installing the new fans in the system and booting the system up, my link and icue software was only showing ports 3 and 4 being used on the copro. On top of that, the max rpm was only running about 800, when the fans should handle around 2000. I tried everything I could think of including: uninstalling and deleting configuration files; re doing all of the wires in the tower; rebooting my system; rolling the software to previous versions. Nothing has worked for me. I plugged the fans back into the motherboard until I resolve the issue. I just hope I didn't fry the copro somehow. Any help would be greatly appreciated on the matter. Thank you.