Yes, since the beginning...
Does it matter whether or not the fan control is set to manual or auto? And are you using CPU as a source?
Are your fans PWM, DC, or a mix? Is your setup using a mix of internal headers and external ones ie. an external fan controller?
I can't recall it ever working for me properly. Temp goes up and the fans (CPU controlled) go right with it.
What is your delay time?
CPU Q-Fan Control [PWM Mode]
CPU Fan Smoothing Up/Down Time [2.6 sec]
CPU Fan Speed Lower Limit [200 RPM]
CPU Fan Profile [Manual]
CPU Upper Temperature 
CPU Fan Max. Duty Cycle (%) 
CPU Middle Temperature 
CPU Fan Middle. Duty Cycle (%) 
CPU Lower Temperature 
CPU Fan Min. Duty Cycle (%) 
Chassis Fan 2 Q-Fan Control [DC Mode]
Chassis Fan 2 Q-Fan Source [CPU]
Chassis Fan 2 Smoothing Up/Down Time [2.6 sec]
Chassis Fan 2 Speed Low Limit [200 RPM]
Chassis Fan 2 Profile [Manual]
Chassis Fan 2 Upper Temperature 
Chassis Fan 2 Max. Duty Cycle (%) 
Chassis Fan 2 Middle Temperature 
Chassis Fan 2 Middle. Duty Cycle (%) 
Chassis Fan 2 Lower Temperature 
Chassis Fan 2 Min. Duty Cycle (%) 
Allow Fan Stop [Enabled]
I use manual. CPU and case fan use CPU as source.
CPU fan is PWM, case fan DC. All headers from mobo.