@AlphaTheFirst - HPET is in Advanced >> PCH Config. If you can't see, let me know, I will check again
* I found the issue! Here is BIOS with more XHCI options enabled too, maybe one of those is causing the auto-reset. There should be one more XHCI at Advanced (XHCI Legacy Support) >> USB and then more at Advanced >> PCH Config >> USB
One that caught my eye at PCH Config >> USB was this >> XHCI Disable Compliance Mode

Hmm! Give me some time on this one, having issue on rebuild now, previously it was easy workaround, but now it's being a pain
I'll keep at it, sometimes I have to walk away and then once I come back it rebuilds properly first time without requiring a huge dance around padding issue

@Lost_N_BIOS Let me know if you need more pictures from bios, i can only see XHCI in Advanced >> USB , no HPET or other XHCI's sadly. Im already greatful for what you have done so far, and i got time so i can wait.
And sorry i didnt know my bios was so complicated but i learned one thing after i saw what XHCI did to my mouse even in that short time until boot; Never gonna buy asus mobo again !

HPET = High Precision Timer and it's located at Advanced >> PCH Config, but if you do not see now, then it may be one of the issues I fixed the other day along with adding what I mentioned above, just need to find way to rebuild this BIOS without breaking it again
If you have flash programmer I can send you BIOS without that hassle to test and see if padding added/removed bricks your BIOS, if not you have to wait until I can fix properly.

Trying to redo it again now

@AlphaTheFirst * Edit - Got it See, just needed to walk away for a bit It's such a painful dance sometimes
Some days I can try for hours to work around this issue and no luck, then next day Boom same stuff with fresh eyes / fresh try and done!
https://ufile.io/13o4dgb1

You should now see HPET (High Precision Timer) @ Advanced >> PCH Config
And there is now more XHCI options enabled too, maybe one of those is causing the auto-reset.
There should be one more XHCI at Advanced (XHCI Legacy Support) >> USB and then more at Advanced >> PCH Config >> USB
One that caught my eye at PCH Config >> USB was this >> XHCI Disable Compliance Mode

@Lost_N_BIOS I dont have to do all the steps again right ? All i have to do is FPTw.exe -bios -f biosregnewM2.bin ? I dont want to do anything wrong

Yes, that is correct

Its giving me Error:368 again, i thought we figured it out in grub 2 days ago

Did you reflash stock BIOS again? Well, no matter what, you have to redo the grub stuff (do both) again, then do the above FPT Flash, that's all.
setup_var 0xEE1 0x0
Then enter
Then >> setup_var 0x8E5 0x0
Then boot to windows and >> FPTw.exe -bios -f biosregnewM2.bin

@Lost_N_BIOS
Im also posting here beside PM, so we dont get confused. I did everything again, grub was succesfull, flashed new bios FPTw.exe -bios -f biosregnewM2.bin ,, now i can enter bios, can do anything but when i try to go Advanced >> PCH Config my bios freeze, i cant use keyboard and mouse the second i click to that option. Tried 4 times to make sure i can click everywhere but only not there(also unplugged then plugged mouse,keyboard) it only happens when i click that spesific section.And i have to mention this i had not reflashed my stock bios before i did all that since you asked above.

edit: Also Xhci-legacy support option is not added aswell,adding the picture
edit2: Flashed the old one you made, added the picture of Advanced >> PCH Config like you asked in pm

@AlphaTheFirst - OK, here, please test now and let me know if -
You now see HPET (High Precision Timer) @ Advanced >> PCH Config

And there is now more XHCI options enabled too, maybe one of those is causing the auto-reset >>
There should be one more XHCI at Advanced (XHCI Legacy Support) >> USB and then few more at Advanced >> PCH Config >> USB
One that caught my eye at PCH Config >> USB was this >> XHCI Disable Compliance Mode

If you cannot see the following let me know >> Advanced >> PCH Config >> USB
https://ufile.io/21bt0v4r

@Lost_N_BIOS Yes, i can see all of them now, - but now i can safely disable hpet(disabled in bios but still not disabled in windows idk why)
-I can disable XHCI Disable Compliance Mode no errors

-As we know before i couldnt disable XHCI Hand-off, and i find out that was because XHCI Legacy Support was enabled(did so many trials)

-But now when i disable XHCI Legacy Support with XHCI Hand-off , i cant get in bios anymore, it just disables my mouse and keyboard during boot(tried this 5 times with different variables, i had to clear cmos every time)

I dont know why they forced my bios to work with XHCI only, this is the first time i see this kind of thing. Im thinking it might be related to EHCI(usb 2) options maybe ? Because they hide them in my bios aswell

edit : Okay so i was out today and bought second hand cheap old ps2 keyboard just to log into bios without having to reset cmos so i can test better :D
Even if i disable XHCI Legacy Support/ XHCI Disable Compliance Mode then go to bios with ps2 keyboard, XHCI-Handoff seems like its enabling itself. Is there any other XHCI's in my bios or EHCI or something related to this(Maybe i should enable EHCI which is hidden in order to completely disable XHCI ?) Or its just motherboard being ridicilous ?

@AlphaTheFirst - Here in this thread is my testing about HPET, see this BIOS Mod I made, under "change log" area see HPET image and click it.
This shows HPET disabled/enabled in BIOS and or in windows using BCDEdit, and which is best (ie best to leave BCDEdit alone, and do not disable windows-side - this is due to Win10)
[OFFER] Gigabyte Z390 M Gaming UPD + Completely Revised Blue Theme

So, you got the XHCI issue sorted now, since you have all the other options? If yes, great! Ohh, sorry, I see still issue! Did you test with that one setting I mentioned >> XHCI Disable Compliance Mode

You should be able to see all XHCI settings now, compare your BIOS with BIOS dropped in AMIBCP to see if any missing.
Yes, we can make visible EHCI stuff too if you need? I don't know anything about messing with either of these, so I can't advise you on what would work for what scenario etc.

@Lost_N_BIOS -Yeah i have been trying stuff about hpet aswell , seems like its different for every computer. HPET doesnt effect much on me except little fps to be honest(I was just suprised it was looking enabled in device manager after i disabled in bios,in my old motherboards it always showed disabled after that) Oh! you also mentioned it in your thread ; ''I was unable to make HPET option visible and function properly for some reason (or maybe I was not testing properly?)
I can make it visible, but no matter what CPU-Z Timers and clocks remained same with BIOS option enabled or disabled.''

-Yes i tested, i disabled XHCI Disable Compliance Mode but for some reason my all ports being controlled by XHCI even after i disable every single one of the XHCI settings(Probably Windows10 doesnt allow them,or i have to select other controller like EHCI) And thats probably the reason why my keyboard and mouse doesnt work until boot if i disable them all.

-I can see all XHCI's now, i hope there is no more than 3 ,you know better than me there shouldnt be Wish i could see every locked/hidden setting in my bios in order to help you more.

-So i think i need all EHCI stuff also(I was actually thinking about this when i started this thread but didnt want to make you hussle:). So i can choose EHCI after i disable XHCI's and try to run every port in Usb 2.0 speed. This one i found from someone who has same problem ; ''I believe that the reason they are both there is because some operating systems may have problems with the XHCI. These operating systems need the EHCI to be enabled and the XHCI disabled.''

@AlphaTheFirst - That was probably also old windows, not Win10

As for the comment I posted about that BIOS mod and HPET how I couldn't make visible, that was due to I was not testing properly before I gave up on that actual visible edit and did the hard mod instead (and it's very tough edit to make visible, huge waste of time when I can just offer BIOS with enable/disable)
I've never looked at Device Manager in any of my HPET testing, so this is unrelated to what you mention

I don't know about XHCI/EHCI, look in BIOS in AMIBCP and see if you are still missing anything. If you need EHCI stuff made visible I can do that too, show me what all you can see now for EHCI @ Advanced >> USB
This is all that's possible there


However, I see this in hidden debug area, maybe you need changed?
USB Keyboard and Mouse Simulator = Disabled
USB Support = Partial Initial (Other option disabled, or Full Initial)

@Lost_N_BIOS - Yeah i forgot to edit my post about HPET sorry, i disabled in bios and enabled in windows and my timers were exactly like yours(lowest possible at the moment) So thank you for that !

-I downloaded AMIBCP (I had no idea i could help you through there , now i feel like i discovered a new planet ) I checked every single page in my BIOS and found some stuff that can cause my lag(added below)

-I can see Keyboard and Mouse Simulator already(I tried it enabled and disabled before no changes unfortunately , but cant see USB Support in my BIOS.
-I dont know if there are any other hidden options there but im gonna post below all i can see in my AMIBCP(the ones which are possible to make input lag), also im suprised EHCI has only Hand-off option.

Ai Tweaker - Asus MultiCore Enhancement
Advanced/Cpu Configuration - Hyper-Threading and Hyper Threading Technology
Advanced/Cpu Configuration - Execute Disable Bit
Advanced/USB Configuration - EHCI Hand-off // USB 2.0 Controller Mode // USB Support (Since you made all my XHCI's and HPET visible i didnt add them)

Adding the pictures (I suppose you have Advanced/USB Config so i didnt add it)





Sorry again for the hussle, once again i didnt know i could use a program like AMIBCP to help you, i had no idea that i could see hidden settings in my bios myself.

late edit: you mentioned ''USB Support = Partial Initial (Other option disabled, or Full Initial)'' if this setting stays default at Partial Initial(in amibcp i can only see that its enabled) this might be the reason im forced to choose xhci.

USB Support (if you mean one not in debug (folder with no name) then it's not visible because it's not necessary, unless you want to fully disable all USB? I can make visible for you if you want, but that's all it does.
Hidden settings would be ones you see in AMIBCP, but do not see in your BIOS.

Please put all images in a zip, thanks! And then, I'm not sure what your list is above, is that stuff you see missing and want?

On 'USB Support = Partial Initial" What do you want that set to? This is a hidden debug setting, can't make it visible but I can change it to whatever you want.