Whenever I use user-defined automatic fan control on MSI Afterburner, the GPU fans ramp up to around 2000 rpm for about 1-2 seconds and then fall back down to the appropriate speed (see first 3 attached pictures).

This only happens when I open MSI afterburner. By default the GTX 980 doesn't start its fan until the temps are about over 60C, so the fans are fine until windows starts up MSI afterburner. I tried turning off start with windows. The GPU fan remains at 0rpm (this is normal) until I open MSI AF myself.

I tried v3.0.1 MSI AF and also EVGA Precision, same thing happens. It only happens when the computer (or I) open MSI afterburner/EVGA Precision for the first time until reboot (with user-defined automatic fan control).

Since the GPU fan is fine when I turn off user-defined automatic fan control, and it only happens once every reboot (when MSI AF/EVGA Precision opens), I came to the conclusion the user-defined fan control is causing this.
I'm not sure when it started happening, but I am sure that it wasn't happening before. Has anyone have this issue? I'm on nvidia 350.12 driver.
 
Someone over at Tomshardware told me that this is normal: "it will rev the fan at the beginning to test it its not a bug."  But I'm pretty sure about 4 days ago, when I startup my computer with MSI-AF, I didn't hear loud fan noises..
 
It should normally look like the 4th attached picture; the fan RPM starting at 0 and then curving to the appropriate speed.

Sajin
Have you tried uninstalling ab, uninstalling the graphics drivers, installing latest graphics drivers, reinstalling ab? 

Just now, I uninstalled AB and RTSS, and then used DDU to uninstall graphics driver. I then did a clean install nvidia driver 350.12. Restarted. Then installed AB, then restarted again to test fan. It was normal. the fan RPM curve was what it was suppose to be.
 
Then proceeded to shutdown system, rebooted to test fan again, they ramped up.

 
350.12 isn't the latest driver, but before I did this, I had 353.62 installed and it still did this.
 
The temperatures are fine, and even the Fan speed % shows the correct percentage (according to the user-defined fan curve). See this picture: 

The fan % will say 30% (which should be the correct percentage for 40 degrees C) but the RPM is actually at 1950 at that point which is clearly does not match the fan speed %. It only lasts 1-2 seconds before it falls back down to the correct RPM.

It's probably just normal. I wouldn't worry about it.