(UPDATE) TONIGHT I AM GOING TO REVERT TO 1.04 AND PUT MY HYBRID KIT TOGETHER 1 LAST TIME IF THIS WORKS I WILL REPORT IT TO EVGA! THIS IS JUST MY ANGER TOWARDS NVIDIA MAKING A FOUNDER's :)
(UPDATE 2) FAILED ON 1.04 DOING THE SAME THING FANS RAMP UP WHEN CLOCKS GO UP HIGH TEMPS LAGGY SCREEN, I AM DONE PUTTING 1080 TI FOUNDER'S EDITION BACK ON AGAIN! 
(final UPDATE) I AM NEVER TAKING MY 1080 Ti APART AGAIN, I WILL MAIL ALL HYBRID KIT PARTS TO EVGA TO DISPOSE OF THEM, CONCLUSION- IT COST 160 TO STAY COOL THIS SUMMER, HAPPY ENOUGH FOR THAT!
 
I was one of the first batch to get the 1080 ti hybrid kits last spring, the hybrid kit worked amazing all summer long no problems. Then it seems after updating a bunch of motherboard stuff end of summer shutting my pc down and starting it the next day causes my hybrid kit to go all wacky, temps ramping up, frame drops, high fan on rad. Putting the founder's edition cooler back on fixes the problem. Not what I want but all I get for now. This is where it gets fun!
 
I send RMA to EVGA and then send my whole box in, they send me the pump. I then ask them to send me the rest of the stuff I don't have, get an email first class shipping, 1 day later wrong stuff, this happened 2 more times before the right parts were sent to me. I have taken my poor 1080 ti founder's edition apart so many times I feel like a pro at taking apart a GPU, time me.
 
So after all this I am guessing that it is one of the last two BIOS updates for the Classified K this summer. I am not a PC pro but I do have a high end pc I built myself. I would like for my hybrid kit to work again, I will take my GPU apart for the 5th time if I know it won't do the same thing. I am afraid of taking my gpu apart which is why I don't want to try anything more.
 
I am about to smash all the hybrid kit parts with a hammer just so I am done with it and would satisfy me. Support cant help, I cant help, anyone can help?
 
 
Edit in my next dream build while I wait. I will be going for a aftermarket gpu from now on no more hybrid. FTW ICX or classified. I want to get the canonlake cpu but I am lost between going ASUS for MB or EVGA again. This is what I want my new specs to be:
 
ASUS ROG MB
ASUS 4k 120hz
Intel 9700k* unknown
Volta top card
platinum PSU
32GB lower speed ram this time maybe 2500-3000mhz with better timings
tighter chassis online pc
even better than my 3 samsung ssds

Have you tried switching to your secondary BIOS? If you only updated the one BIOS, the secondary BIOS should still be as you got it from the factory. Of course you will have to reset any custom settings, such as boot order, XMP memory profiles and the like. There is BIOS select switch on the right hand side about half way down the board I think. It shouldn't cause any issues with Windows as long as you make sure the settings are all the same. So I would suggest take note of all settings in BIOS 1, switch to BIOS 2, change settings to as they were in BIOS 1, and see if this fixes your problem. Since you have a skylake processor, there isn't really a need to have your BIOS upgraded beyond 1.04 (unless the newer BIOS versions also fix another issue you are having). I run 1.04 without issue with an i6700k Skylake.

I thought the same thing Sajin but the RMA did the same exact thing. IT worked all day the day I installed it, shutdown pc go to sleep and wake up to a restart that makes the hybrid kit go wacky. The only thing I have changed is XMP profile 1, all rest of BIOS is default.

Hey thanks Cordorb for reply, I tried it all, my founder's edition just doesn't want to accept a hybrid kit anymore. Maybe my 1080 ti is overplayed this summer and too much thermal pad sweating, oh well all is over now, it still plays fine with founder's cooler on, just no more overclocking.

Hey Cool GTX, I do believe its a bug in my founder's edition. I think i drove it in the ground, one thing I noticed is my hybrid kit was making the thermal pads sweat and oily fluid was visible through the PCB. Note that.
 
I was using MSI Afterburner all summer, +150 base, +300 mem, the thing is that doesn't kick in til windows opens. The fans were ramping up on first bios splash screen.
 
I will talk to gigabyte about my founder's edition, they are the labled dealer.
 
Windows 10, always updated.