Speedfan literally turns my fan off after replacing my fans
I would check voltages, but thats a really hard and dangerous task with short circuiting possibilities. If you are brave enough i will tell you how
Firs set the control to 100% and check the voltage with a multimeter, place the ground lead in a GND connector of an unused molex or the chassis of your PSU and with the positive lead touch the Positive connector on the PWM connector, it should give you a 12v reading, more or less
Now set the control to 50% and check voltage again, it should still give you 12v because PWM does not control based on voltage, if you have 12v means that your + pin on the header is OK, now invert the leads, place the positive lead to a 12v (Yellow) connector on a unused molex and with the negative lead touch the GND pin on your PWM header, if it gives you 12v it means its OK too, if any of that tests fails, it mean the problem is your MB but that would be unusual.
Now, you should check your MB fan control configuration, enter the BIOS and set the control off if you can, i have a ASUS M5A97 R2.0 and it let you turn the control completely off, and even with the control ON, speedfan overtakes that and control the fans on its own without the MB controller involved
If you still have the problem i think the problem is speedfan itself (RARE i have used speedfan for like 2 years and it never happened to be speedfans fault if anything is wrong)
Press the configure button and you SHOULD have these configs:
In temps tab make sure you have the right temperature desire set. If you have a very low desire temp maybe speedfan is setting 95% as minimum speed
In speeds tab make sure the minimum speed allowed to the fan is 20% (or a speed you are comfortable with) and its NOT set to automatically variate (that is why a custom fan curve is prefered)
In fan control make sure you are running a custom fan curve adjusted to your cooling/noise needs based on your MAX of speeds
In advanced tab make sure you select your correct MB chip and the fans are set to SOFTWARE CONTROLED and checking the "remember it" option
That should do it, i hope you can solve your problem using this information
PS maybe you can check speedfan first, before atempting anything with a multimeter and risking a short circuit
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