EDIT2:
I was able to run the graphics card in the first slot by changing the PCIE generation to 2.0
After changing to generation 3.0 or 4.0, the board does not detect the graphics card. Clearly the problem lies with the motherboard. Does anyone have an idea what's going on? As a last resort, my question is what is better: gen 2.0 x16 or gen 3.0 x4?
Please read this until the end.
Could you try nvflash (download it, unzip it and copy to C)?
you should try this command (since there is 2 pcie cards) step by step:
run cmd as admin, type cd /x64
-nvflash --list and see which index is the 1080, this is for example:
-nvflash --protectoff
-nvflash --index=(index of 1080) -6 biosname.rom
Here is 2 rom, make sure to choose one of them which matches all the IDs
https://www.techpowerup.com/vgabios/191740/MSI.GTX1080.8192.170330_1.rom
https://www.techpowerup.com/vgabios/191386/msi-gtx1080-8192-170330
They have different SHA and MD5 hash, but everything the same, just make sure you pick the correct one, if there is no checking, then go with either both of them
Also before you do this, Disconnect from internet, uninstall nvidia drivers using DDU, proceed to device manager and go to processors, uninstall all of them (should be 24 in yours) and uninstall them like this (when it request for restart just click NO and proceed uninstall the rest):
After that reboo to bios, and proceed update the mobo bios (while 2 cards are still there)
to the latest, then load optimized/default settings, save and exit, boot to windows and install the latest
amd chipset driver, then reboot to windows again.
then proceed doing the nvflash steps above.
after doing the nvflash, reboot to windows as instructed, then reboot to bios, and set the x16 to pcie 2.0 since it's the last known work mode for 1080, save and exit, then shut down, change the 1080 to top slot, and try if it boots fine.
If it does boot fine, try to go to bios and change it to pcie 3.0 or auto. and if it worked, then proceed go to windows and install the latest driver. also check for the latest windows update and optional updates, install them all.
I hope you understand
Make sure the psu connected to the gpu is 1 pcie cable per 1 slot (use main cable, not the branches/split) like this:
Also check in the graphics settings if there is Hardware Accelerated Graphics Scheduling, and enable that then reboot the pc.