Bypass the molex altogether and see if that helps.
Basically what I can see is this: 3wires from Controller: the Red and Black are your power and the yellow is still your rpm?, but a schematic for that should be included.....
Even though it is a 4 pin connector, you should still have only 2 wires going to it from the power supply right? So you can either hook up the red wire or the yellow wire to feed power, not both at the same time. [Yellow is preferable, since it's gauge is probably rated for 12v's]
The 4 pin is really for a computer connection and that is why it has two Separate rails for + power. You are just working with one leg 12V+.