I have this CPU Cooler and had similar issues. First thing for me was on the FanMate. The knotch on the knob was not on the same side of the circle as the arrow point which way was faster. That confused me a little at first, but after playing with it I realized that the clockwise/counterclockwise instructions still held true. Turning the knob fully counter-clockwise sets the fan to operate in silent mode, while turning it all the way clockwise sets the fan to operate in normal mode, or full-speed. The farther clockwise you turn the knob, the faster the fan will go.
Now, from what you are saying you probably ran into the same issue I did. You tuned the knob clockwise and it got slower and finally stopped instead of speeding up. This is because despite having the FanMate attached to the Cooler, your Motherboard's fan controller is probably still controlling the speed of the fan. If you have adequate cooling on your case and your CPU is idle, your motherboard will probably decide that the fan does not need to run at all. I had to go into my BIOS and disable SMART Fan support so that the FanMate would be able to completely control the speed of the fan on this Cooler. Look around on your BIOS and you'll probably find a similar solution. Just remember that if you disable this setting, you need to make sure that you have manually set the fan to an appropriate speed for your CPU for when it goes under full load.