I don't have any external or 3rd party controllers to regulate fan speed.  This also includes software controllers as well.  My dilemma is this:
 
I am currently running a X99 Classified MOBO.  In the BIOS, I have set my fan curves to my desired speed.  They work great. . .when the PC starts up and actually kicks them in.  It usually takes me like 7-10 shutdown/restart attempts to get the fan curves to actually work.  I'm sick of this.  I've tried everything, including turning them off in the BIOS, quick restart/shutdown, and they are still running!! WHY!?  I don't get it.  I've set everything to 0% fan speed and theyt're still running: 100%.   I've updated the BIOS, updated every single driver associated to the motherboard from the software/driver page.  For the life of me, I can't get the PC to boot up with MY fan curves.  It automatically just puts everything at 100%, including my GTX 1080 Ti(s) in SLI.  My PC sounds like it's on a mission to Mars.  Is there anyone out there who can assist?  I'm about ready to chuck this PC into orbit so it can make its mission.

Post your BIOS screen shots
 
What are your fans ? 3-pin or 4 -pin
 
Which MB connectors are you using ?

Close all background programs and recheck the fan speed. 

That sounds like there is a program that is causing this.
 
There is a couple of things that you can try - install Windows on a different partition or a different drive to see if the problem goes away. If it does, you need to figure out what program is causing the issue. It's one that loads with Windows, so you can always uninstall one at a time to see which one it is. it could just be an updated version that causes this behavior and needs to be reported to the developer.

Mazraku
The fan on my 980ti Superclocked has stopped responding to precision and runs at 100% even with nothing running. I can't slow it down in any way shape or form, I have turned off auto and tried manual speed but it just keeps going at 100% I have rebooted a few times, I turned the computer off and back on. It was working fine an hour ago and when I started Arkham Knight it went mad and wont stop..Any ideas on how to fix this? Sounds like a friggin washing machine. P.S according to precision my fan in at 0rpm 

You really should start you own thread in the 900 series forums: https://forums.evga.com/EVGA-GeForce-900TITAN-X-Series-f99.aspx 
 
That said, it sounds like the fan controller is going out. You can try to reseat the video card, reseat the power cables going to the video card, and try reseating the GPU fan plugs in their headers. 
 
A clean driver install using the methods in step 2 here might help.
 
Make sure you only have one monitoring program open. If you have multiple programs that monitor and / or control fan speed open, it may be causing this problem. Close them all and test.
 
If all those steps fail to help then you likely have a fan controller going bad and will need to start an RMA. Register your card here if you already haven't, then open up an RMA by calling or emailing EVGA here (or start the RMA from the My Products page). If you aren't the first owner of this GPU you are still covered under a warranty that began when the card was manufactured, and can register for the RMA here.