Depends on exactly what model of GTX 980 it is, need to know that, it matters..Maybe see: Why are the fans on my 900 Series ACX 2.0 cooler not spinning?
 
Uninstall PrecisionX..Then delete the Program Files (x86)\EVGA\PrecisionX 16 folder..Then install the latest version of PrecisionX..Then go to the General Settings and select "START WITH OS" and click OK..Go from there.

Is this issue only happening with the latest Precision X? If not make sure that you go to General Settings and enable "Start With OS" [See img attached]

stalinx20
Not trying to hijack the thread, but when you set certain settings, such as FPS limiter, and then close the software, the limiter is still "running". Does it still keep the overclocking settings as well?

Yes..You can see that in the GPU-Z Sensors tab.

Well it would not auto start even when you select "Start with OS" in the PX16 settings.  I had to manually drag a short-cut icon into the Windows 10 start up folder.  Even though this is a 980 GTX ACX 2.0 and the fans should start automatically at 60 degrees C. It didn't. Now that I have it start at start up, I have full control over the fans.  I don't think this GPU ever worked properly from the day that I installed it.  I remember even subtle tweaks caused a crash of the system and I backed off and settled for stability.  I am hearing fan sounds I never heard before.
 
This all started a couple of weeks ago.  It started crashing and I would go into Windows Event Viewer and saw so many reasons/error codes why it crashed and never once did I consider the fans. I gave up and ran Recovery in Windows 10 which is like a complete re-installation and I still had a crash after that. When I googled the last error I got a lead that indicated issues with this model and Precision X16. I started working though Precision's options and determined it was not working as intended.  I never considered the fans and really, since they are facing down in my case, you really could not see if they were working or not at the time of the crashes.
 
I am please to say (knocking on wood), I am currently stable and I even tweaked the GPU a bit, played a few games to test.  I think I am good.  But this was one of the most intense trouble shoots I have done with my computer with all the error codes in the Event Viewer.  I have built a number of computers over the years and this is a first for me.  I have a feeling though I am not going to purchase EVGA in the future.

If all else fails, shutdown completely, open the case and re-seat the gpu and psu cables connected to it. And yeah, MSI AB or bios mod so no oc software is needed.

I am a simple man and a minimalist. PX is great, but I like the simplicity of AB or like stated above, no SW at all. Awww no more Dark Angel avatar :(

Oh, didn't realize we could do that, lol.

I have 4, lol. Is there a way to change the tag under my "avatar" to" FTW+ Member"?

I learned 2 things tonight, thanks. Only 282 posts to go.

 
 ^  Sajin is correct. That's your only choices.      =)