Are they plugged into case fan headers or some sort of fan controller?
I assume they are 4 pin PWM fans, if thats the case it may just be one of the fans is less sensitive and wont fire up until it gets a certain amount of signal.
If you can find the fan control settings in BIOS does it come on if you set all to run 50%, or 100%? If so I wouldnt worry about it, its just that all fans arent created exactly equal, the fan that isnt spinning will come on when its needed. If it bothers you can probably set a custom fan curve and raise the lower range a touch until it gets to the point it engages.
If not you could try switching them around to different ports to see if its the fan or the port on the motherboard.