The motor shield is rated for 1.7amps but your fan is almost the double with 3.3 amps :  https://github.com/SHWotever/SimHub/wiki/Arduino-Shake-It#adafruit-motor-shield-v2-or-clone. 

When it's overloaded the shield will overheat and internal security will simply cut power.

The monster Moto shield will allow you to hold such power (6amps max)

I am having this weird issue. When i accelerate to around 30kmh, the fans go crazy to full power and shut down, after a second it goes full power again until i stop.

my hardware, arduino uno with adrafruit clon, 5300 rpm 3.3A fans (NIDEC BETA V VA450DC V34809-90 120x38 12 VDC 3.3A FAN). My power supply is 3A therefore i use only one fan for now.

Things i tried: 5a of power supply : i was able to increase the power for a little bit but not much.

Increase pwm : it worked well actually but still i have to decrease the power around 25. by the way, when i put the pwm to 400, it cannot start the fan until %50. 

Now, it works with 950 PWM but the speed is too slow and global gain is at %25.

How to solve this ? thanks