Solid reliable Fan Controllers: Sunbeam Rheobus Extreme (Mod the leds) or Lamptron FC-5.
Well, I've never owned a NZXT product and generally tend to stay away from the brand from what I've heard (check newegg reviews), but anyway:
Check the fans. Can you switch them around and test if they work on other channels?
What Ampere ratings are the fans? Are you running some Kaze Master 3000 rpm fans or silent slowrunning Noctuas?
Depending on the version, your fan controller can handle 4-6W/Channel apparently. Some fans might require more than that. Most don't. Just to compare, the Lamptron/Sunbeam can handle 30W/channel.
Also is there any fan controllers that have 4 pin fan connections instead of only the 3 pin?