So at first both cards LED would go out and shutting down the computer and turning it back on would solve the issue. The bottom card is completely fine now, but the top card's LED will randomly start blinking then turn off. Shutting off the computer and turning it back on is the only way to restore the LED. 
 
Now another weird thing is, I cannot control the LED anymore for card 1. Also, in the classy voltage tool, the first card has a different option at the bottom, as can be seen in the pics. 
 

 

 
Here's a video of what happens: https://vid.me/K1VU 
 
Also I did a bench at 15XX/8000 : http://www.3dmark.com/3dm11/10548971 
 
and 15XX/8400: http://www.3dmark.com/3dm/9404366 
 
Do those scores seem right?
 
Thanks 

Can you at least control the LED once you turn off the computer and back on?
 
Also does your classy controller show the same options for both cards? When I originally got the cards, both cards had the same options but after the LED turned off it hasn't gone back to the same and I haven't been able to change the LED. 
 
Might just return the cards if EVGA didn't help you either. Wonder why it happens. 

Sajin
Are both the cards running the same vbios? If not, try flashing the vbios from card 2 onto 1 to see if it fixes the options issue.

Yeah same vBios on both cards, I tried all three vBIOS' on both cards and still the same issue. What concerns me more is the fact that I can no longer control the LED and that the first card has PWM freq now instead of OCP and Vdroop. I feel like there may be a underlying problem.
 
Also does it look like the cards are performing fine judging by the benchmarks? The Firestrike GPU score seems kind of low to me.  

ssj92
Can you at least control the LED once you turn off the computer and back on?
 
Also does your classy controller show the same options for both cards? When I originally got the cards, both cards had the same options but after the LED turned off it hasn't gone back to the same and I haven't been able to change the LED. 
 
Might just return the cards if EVGA didn't help you either. Wonder why it happens. 

Yes, after rebooting I can control the led's with PX. If I do not restart the controls are blacked out and nothing can be changed.
 
I have to manually set both card's for it to work.
 
EVGA is normally very helpful but with this issue they started to help then just never answered my phone calls or emails.
 
There is a how to that fixes the led flicker issue, it's on the kingpin forums. However I do not fill comfortable doing that and I also feel like with the led's turning off and not being able to control until the system is rebooted there must be other issues going on.
 
I have not looked into this since end of summer, so let me know if you find anything out.
Thanks