I was dumb and updated my F5 bios to F7 just because I wanted it to be newer. It introduced the PCI-E Gen 3 bug, which causes PCI-E1.1 style performance with terrible stutter and 50% FPS on some boots, and even totally failed cold boots (only fans spin but nothing else happens) requiring pressing reset to boot up fully. Gen 2 setting works flawlessly, but obviously it is eating up my 1080 Ti performance a little.
Specs:
Z97X-Gaming 5
2x8GB Kingston DDR3 1866MHz
Palit 1080 Ti Jetstream
Crucial MX100 & MX300 500GB SSD's
Seasonic P-660 platinum
I have
*changed the power reset kit on case with a spare part
*changed CMOS battery
*removed soundcard from the PCI-E X1/X4 slot
*flashed F6 and F8b bioses
*reset BIOS settings
*tried changing the PCI-E DMI Link Speed setting
*reinstalled Windows 10 a few times (was a long shot, since problem behaviour shows up in BIOS already)
So, any ideas? There quite a few mentions about this Gen 3 PCI-E cold boot bug around the internet when you dig up, but Gigabyte support acted like this isn't reality, and didn't care about a motherboard that is older than 2 years.