Hi,
I had a similar problem with my 980 SC, probably there is just the wrong BIOS installed.
Please check the card and verify you have the "04G-P4-2982-KR" model.
 
If that is the case, contact EVGA and ask them to send you the correct SC BIOS. You can easily update the SC BIOS with NVFlash afterwards.
Alternatively you ask them for an RMA, but I guess changing the BIOS would be much easier!

EVGA asked me if I want to flash the BIOS on my own (without losing warranty) or offered an RMA.
I decided to flash on my own (they sent me the BIOS rom) which worked just fine.

You can find a tutorial here:
http://www.overclock.net/t/1517316/extract-and-flash-gtx-970-and-980-firmware-nolimits-and-gamestable
 
Use the custom NVFlash version (JoeDirts's 5.196) and the BIOS you got from EVGA and follow the Flash Guide instructions.
 
(I strongly recommend to only flash an official EVGA BIOS. Also make sure you got the permission from EVGA to flash the BIOS on your own without losing the warranty!)

@Vlada011: The BIOS file from EVGA for the 980 SC got a different MD5 checksum in comparison to the one you posted. 
I would ask EVGA for the official .rom they are using to flash the cards (just to be sure)

What doesn't work?
I see now on overclock.net
 
He need to try with command nvflash -4 -5 -6 .rom 
I flash on that way my card but Yes you are right here is whole explanation for Maxwell even with Bootable USB.
 
http://www.overclock.net/...ia-gtx-980-owners-club
 

Off course I would ask from them BIOS and recommended Tool.
I do this because I have 2 BIOS, and Normal (1st) is always default.
Because your card looks different. 
This should be GPU-Z Specification for
GTX980 Superclocked (04G-P4-2982-KR) 1241MHz Base Clock and 1342(1392) Boost Clock.
 

 
Your GPU-Z Specifcation show
GTX980 (04G-P4-2980-KR) reference with 1127MHz Base Clock and 1216 (1278) Boost Clock
Compare Default GPU Clock and Boost Clock with your GPU-Z.
 

I still think EVGA forgot to flash their own modified BIOS on your card and the one you see is the reference Nvidia BIOS.

I think same, that card somehow pass without flashing with any EVGA BIOS.
Mistake probably. When you flash with proper BIOS for your card you should test careful because
card will be 115MHz overclocked than with same voltage as now. That's reason because you saw lower boost clock.
Good luck. 
 

@vlad: You are absolutely right, I didn't think about that yet.
One more reason to make sure you got the permission from EVGA to perform that flash.

As I said before you could also request an RMA and get new card, but thats your choice.

You will get at least +1000 on Graphics Score in Firestrike benchmark with right BIOS.
This is your BIOS 100%, don't flash him, only download...
 
http://www.techpowerup.com/vgabios/162173/evga-gtx980-4096-140910.html
 
Should work, 980 OC nice.
Because you have completely wrong BIOS inside. 
Even guys with GTX980 reference have EVGA BIOS.
Where you bought card? Ask them to help you, maybe they could assist you.
 
See specification of BIOS and how much boost, as you ask 1342, but in games she boost more on 1370-1390MHz I think...
 

 
3842 is Subvendor EVGA 
2892 is Part Number 04G-P4-2982-KR
 
And after flashing GPU-Z will show this
 

 
 I would contact EVGA and ask permission and help from someone who know in service to flash card with proper BIOS.

BTW the 600 series never boosted to full clocks if you didn't do a full screen.  Have you tried something like Heaven or Valley fullscreen?

No I was saying the GTX 600 series wouldn't show full boost if whatever you where running wasn't in full screen. Also afterburner is a far more accurate tool to use in real time while you run said program to peg your full stock boost.