The fans are each hooked to the sys fan ports on the motherboard. There are 5, so each fan is connected to an individual power supply. I did have a hub that I was powering with a SATA cable, but had the same result.
The LED controller is hooked to a SATA power line and I have tried plugging in each individually, each on a different plug, all in series (plugged into each other using only one port on the touchaqua control board)
How can I test to see if the LEDs on the fan are broken? This was bought brand new from Microcenter, and have never been installed in another machine. As I stated in my first post, when I first hooked them up, they worked fine. It wasn't until I hooked the HD up that the lights on the fans did this.