Hi,
Are your fans BLDC fans?
They may not like PWM as their supply because their speed is regulated by a built in switching system, speed is regulated by the system frequency not by the supply voltage.
That is why they have 4 wire fans, the 3rdwire is tacho out and the 4th is speed in.
The fans will change speed with load from the air flow, all you can do with 2wire fans is keep their supply voltage constant.
Lowering supply voltage will lower speed but also make the speed unstable.
Tom.... 