This is the weirdest issue I've ever had with graphics cards. To begin, here are the relevant specs:
 
 - 2 EVGA GTX 980 HC FTW in SLI. Not custom overclocked.
 - Core I7 4770K @4200 MHz
 - Windows 7 x64 Ultimate on SSD
 - Asus Maximus VI Extreme with Latest BIOS Firmware for both BIOS
 
Problem description:
 - sometimes after starting the PC, all games and benchmarks perform at 50% of normal FPS. SLI is still active though and all values like temps etc are fine.
 - Latest drivers etc, etc. Problem existent since the last 3 driver versions, but didn't start after installing a driver.
 - After rebooting several times, it usually get's back to normal (rebooted 7 times now with the problem persisting at the time of writing this though)
 - In GPU-z under Bus Interface it says the following for Card 1 and 2 respectively: PCI-E 3.0 x16 @ x2 3.0  and PCI-E 3.0 x16 @ x4 3.0    <-- It looks to me this may be the issue? x16 running at x2? o_________O  
 
If that's the issue: how can I solve that?
I already ran CPU-unparking programs, but this seems to be a GPU related issue. I already reinstalled the drivers with the clean method and driver cleaner.
 
Edit: listing what I tried to solve it after the original post (to no avail):
 - went into msconfig and started Windows in diagnostics mode - no effect, same 50% fps loss
 - deinstalled every recently installed program
 - checked for viruses
 - Turned off Hyper Threading and the internal CPU graphics.
 - Re-seated the cards. This was one hell of work because they are not only heavy but also build together with a water tube between.
 
The last attempt fixed the issue. Cards are at x8 / x16 now.
 
If anyone has the same issue this might help. Also if anyone can and wants to answer: is 8/16 normal for SLI on a Maximus VI Extreme or can they both be at x16?

Forgot to mention that I of course did that and meant the x2 and x4 values from within the render test. They were x2 and x4 respectively before I fixed the problem. Now they're x8 and x16.
After re-seating they are at those values even without the render test being active.
 
Clock speeds were exactly identical when they were poorly performing. Loads too. That wasn't it.

bcavnaugh
Are the Cards installed in the X16 Slots?
Did you set the Bios from Auto to X16 and set the GEN to GEN3
Are you Sharing PCIe Lanes with other Devices like maybe a Sound Card or Raid Card?

Yes.
No and no. Should I do this? Both are on auto. Does that not reliably work?
A Sound Card is on the fourth x16 lane. Is that a bad idea? Didn't check if it can go to the x4. Should I seat it there if that's possible?
 
 
 
Edit: Changed from auto to Gen3. Still x8 and x16 though. Also in the BIOS it gave me the option to enable full x16 on lane 1. However this would deactivate all other x16 lanes.
So I guess x8 + x16 are the maximum values and everything runs fine now, right?

Thank you for the help! I did what you suggested and benchmarks say it was the right thing to do. Of course I also deactivated Hyper Threading while trying things out.
 
Will re-enable that and see if that changes even more now.