As expected f989e55452c74b4f7b22c889b8ec9f1192aaeec4 is a bad commit.
When kernel built with the preceeding commit
 1a131ca1de7a84cf3827c418ee5971b493c6f23f then the fan is well behaved..

ie echo 200 > /sys/class/hwmon/hwmon3/pwm1 
 The fan speed builds up gradually and results in a reasonable constant fan speed fan1:        2207 RPM

echo 180 > /sys/class/hwmon/hwmon3/pwm1 
The fan speed is reasonably constant at fan1:        1118 RPM
 
Note in both bad and good kernel the fan speed is not linear with the value sent to pwm1, rather a step change at about 192 from slow to fast.

In the good kernel the fan speed is rock solid constant.. I could not seem to get the fan to get faster than 2207 RPM

In the bad kernel the fan speed is always varying as indicated above.  When configured with echo 200 >  /sys/class/hwmon/hwmon3/pwm1  the fan speed is always varying about a high value and with echo 180 > /sys/class/hwmon/hwmon3/pwm1 the fan speed is always varying about a low value.  The range of fan speeds seems larger with the bad kernel (3000 -> 300) as you can see from the comment above.


Noticed that in the good kernel the virtual device seems to report the fans in the opposite order:
$ sensors
radeon-pci-0100
Adapter: PCI adapter
temp1:        +57.5°C  (crit = +120.0°C, hyst = +90.0°C)

coretemp-isa-0000
Adapter: ISA adapter
Core 0:       +28.0°C  (high = +83.0°C, crit = +99.0°C)
Core 1:       +26.0°C  (high = +83.0°C, crit = +99.0°C)
Core 2:       +28.0°C  (high = +83.0°C, crit = +99.0°C)
Core 3:       +25.0°C  (high = +83.0°C, crit = +99.0°C)

it8721-isa-0a10
Adapter: ISA adapter
in0:          +0.86 V  (min =  +1.12 V, max =  +2.09 V)  ALARM
in1:          +3.02 V  (min =  +2.87 V, max =  +0.64 V)  ALARM
in2:          +2.00 V  (min =  +2.54 V, max =  +1.44 V)  ALARM
+3.3V:        +3.29 V  (min =  +4.56 V, max =  +4.37 V)  ALARM
in4:          +2.99 V  (min =  +2.68 V, max =  +2.82 V)  ALARM
in5:          +2.22 V  (min =  +2.62 V, max =  +2.29 V)  ALARM
in6:          +2.22 V  (min =  +2.29 V, max =  +2.83 V)  ALARM
3VSB:         +3.34 V  (min =  +3.82 V, max =  +4.54 V)  ALARM
Vbat:         +3.02 V  
fan1:         965 RPM  (min =   13 RPM)
fan2:        1112 RPM  (min =   21 RPM)
temp1:        -78.0°C  (low  = +55.0°C, high = -68.0°C)  sensor = thermal diode
temp2:         -8.0°C  (low  = -57.0°C, high = -93.0°C)  sensor = thermistor
temp3:        -71.0°C  (low  = -77.0°C, high = -49.0°C)  sensor = Intel PECI
intrusion0:  ALARM

i8k-virtual-0
Adapter: Virtual device
fan1:        1120 RPM
fan2:         972 RPM

Notice that in comment #16 the fan speeds are in the same order... apart from the label change.

So with the good kernel it seems that the virtual device thinks fan1 is the CPU fan and the ISA adapter thinks that fan2 is the CPU fan.

With the bad kernel it seems that the virtual device thinks that the CPU fan is called Processor Fan and the ISA adapter thinks that the fan1 is the CPU fan.

Seems to me like someone has switched some labels about!  Perhaps by "correcting the labels" something else has gone wrong!  Perhaps ISA adapter needs to think that fan2 is the CPU fan for some reason!

Anyway thats about all I can see is different from a quick review of the sensor command output.