This is part of another post I just wrote last night:
 

The issue is caused by a design limitation.  The only way to control the speed of a 3-wire fan is to adjust the power input (or ground input) to the fan.  Power input adjustment is utilized by means of varying voltage potential [PWM].  ...  The tachometer feedback circuitry inside the fan is created by means of an inductance controlled circuit which makes and breaks connection between power input and tachometer ouput as a magnet passes by the tachometer sensor device.  If the power input is of varying potential, it causes the tachometer output to be corrupted...
  
Let me illustrate:

 
So, that is basically the problem you are seeing.  Your fan controller is providing a pulsating DC power input to the pump's +12vdc input (yellow wire) to decrease the pump's speed.  The pulsating DC signal is superimposed on top of the tachometer ouput signal which corrupts it and causes the tachometer ouput signal (blue wire) to be misinterpreted by the motherboard.
 
There is another way to slow the pump down to a steady speed without using a fan controller and without corrupting the tachometer signal.  This other method requires switching pins in the pump's molex power connector so that it receives its power from a source other than 12vdc.  If you move the pins around in the connector, you can provide either 5 volts or 7 volts to the pump instead of 12 volts.
 

 
There is another method of controlling the pump using PWM input to the pump via a fan controller which will not necessarily destroy the tachometer output signal, but it will require that you have (basic) electronics knowledge and soldering skills.  Basically, you can incorporate a circuit between the fan controller output and the pump power input which will swap the PWM input to the pump over to the ground side instead of the positive side and may cause the tachometer output signal to be more usable.
 
You would use this design as a reference:
http://www.techpowerup.com/forums/showthread.php?t=115752
 
This is how you would use that circuit:

 
You would have to make sure that the irl530n MOSFET used in his diagram is capable of outputing the amount of current your pump requires.

Krony

That is a pain tho every time i wanna change it :P

You could incorporate a selector switch accessible from the outside of your case to select full pump speed (12v) or decreased pump speed (5v).
 

 
I'm just showing you some options.

Krony

Yea i always thought fan controllers used a variable resister that just dropped the voltage not a pulsating input ...

No, almost all fan / motor controllers use PWM (pulsating DC of some form) to control speed.  You could control the speed straight through a variable resistor (potentiometer), but the potentiometer would have to be designed to handle high amperage and would have to be designed for very low resistance and very low sensitivity (low amount of resistance change from max to min setting).
 
The primary reasons why a simple potentiometer are not directly used to control speed is that they provide a less efficient method of speed adjustment, will get hot, and won't provide a linear speed adjustment.  Basically, if you use only a potentiometer to adjust resistance in the circuit, as you decrease the speed setting (increase resistance), the speed will decrease almost exponentially.  This will make the speed control close to max not very sensitive; and the speed control close to min exceedingly sensitive/touchy.  Also, the pump / fan / motor being controlled by PWM can run at a lower RPM without stalling than the same device could if it were controlled by resistance adjustment only.
 
Primary advantages of PWM versus just using a potentiometer:
More efficient
Observed speed more closely relates to expected results (more linear)
Slightly less power is required and slightly less heat produced
A lower RPM can be obtained without motor stalling
Does not place high amperage load through potentiometer (potentiometers usually burn out easier than transistors)
 

Krony 

i only need a 2 setting switch, 1 for 12v max for gaming benching and another for maybe 7v for general pc use.

Yes, you could make the switch control 12v or 7v (instead of 12v or 5v), but the solution is a little messier since it involves having both ground and a power source going to the same switch (generally not recommended).  It is fine to do, but if the switch fails internally and the two connections bridge at the same time, it will create a short.  But I guess the other design would short 5v to 12v which is equally bad.  Either way, a short should cause the PSU to shut off and should do no damage to your computer.
 
Selector to control between 12v and 7v.