Most likely you need to recap your rom file. Think Ubutool can recap the file automatically.
@loris100
All must sure, that as davidm71 stated, to use Asus BFB its need to be capped, as for UBU indeed it re-caps it again with the option to rename in order to use Asus BFB, the safest way in ur board.
Unless u extracted bios region in UEFI tool
Do NOT use Asus EZ flash utility in Bios
The correct name is X99A.CAP for Asus BFB
Most likely you need to recap your rom file. Think Ubutool can recap the file automatically.
I just deleted CPU microcode patch files with MMTOOL and then saved it so it remained as CAP file, i tried using Asus EZ flash utility in bios and it gives me that not uefi bios error, UBU is a bit complicated and dont resally understand how it works
I told u NOT to use EZ flash…any tool used its a mod file in the end.
Use UBU to update mCode, use MMtool to remove unwanted (Be sure of what u remove!!!) and them BFB to flash.
Before BFB, load default bios, save reboot, shutdown, power OFF AC discharge 2m. Now Asus BFB.
EDIT: So u cant use UBU because u dont want/know how to install Python, too bad. Others can and learn how, getting the results expected.
Lots of info and shared knowledge in this forum, u should take advantage of it.
I told you i dont know how to use UBU, why should i update the mCode with UBU? and what kind of update i should apply? BTW today i tried to flash with bios flashback the MMTOOL X99-A-ASUS-4101.CAP file but it doesnt work, the light keeps flashing every second and nothing happens, can someone help me with this? Need every cpu microcode patch removed, Asus X99A motherboard and X99-A-ASUS-4101.CAP bios name, cant attach it cause it larger than 6MB
EDIT: cant even update the mCode with UBU since its asking for python 3.7 or higher to be installed
Ok i installed Python, had to install few other things aswell, had to install MCE updates so finally got UBU working, now the problem is i did update that MC stuff but i dont understand why i should do that? I want to remove microcode patches to gain performance since they released them to fix some sercurity flaws…Anyway i couldnt find a way to remove those patches from UBU, i just did the MC update saved the bios to X99.CAP and managed to use Flash back succesfully but now it recognizes only 3 cores out of six, its basically a 3 core 6 threads…So by using UBU i did only make things worse…
There are not guides how to use UBU properly for my needs, not here or anywhere else, so just give me clear instructions if you want to help me…
I also tried to remove cpu patches from MMTOOL and then used UBU to save the X99.CAP file but it wont flash…
Check out the Ubutool threads. There are about two novels worth of information on how to use it properly. Theres also a way to use Uefitool to recap the file but complicated for the novice user. Would recommend you post both your
modded rom file and original files for others to look it over. As for how to use flash back there are also loads of info here on how to do. Just takes a little searching time to find. Usual method is to use a fat32 usb key and place your
modified rom on the key and follow naming conventions. Found this table on other site:
X99-DELUXE/USB3.1
X99D.ROM
X99-A/USB3.1
X99AU31.CAP
X99-PRO/USB3.1
X99PU31.CAP
X99-DELUXE II
X99D2.CAP
X99-A II
X99A2.CAP
X99-E
X99E.CAP
SABERTOOTH X99
X99ST.CAP
ROG STRIX X99 GAMING
STXX99.CAP
RAMPAGE V EXTREME
R5E.CAP
RAMPAGE V EDITION 10
R5E10.CAP
And I found this guide from Asus directly:
https://www.asus.com/us/support/FAQ/1038568/
I know how to use flash back and did it successfully many times now, the problem remains and is big now, i even tried to flash stock bios with EZ utility from Asus but my system still recognize only 3 cores 6 threads, i dont really know what happened but its messed up right now
Microcode did not get accepted probably. Start over.
Ok i will try to update microcode again and will update here later 
Just post it so we can take a look before you do just in case.
Ok updated microcode with UBU again, i installed an old bios and had a microcode which was older and without the spectre and meltdown patch (thats what i wanted since the beginning) with UBU i have a newer microcode now which has latest security patches but i still have only 3cores and 6 threads, i will post a cpuz validator
https://valid.x86.fr/2tgiup
Checked actirve processor cores in bios? Tried to reset to bios defaults?
On bios it shows all 6 cores are anebaled, hyperthreading is also enabled, on windows it shows 3 cores 6 threads and benchmarks reflect that…I tried many reset but nothing changes
Try stock bios and see if problem persists.
Tried stock bios and still same 3 cores and 6 threads, i dont know what the hell happened, every bios i flash from UBU with flash back or stock with EZ flash doesnt change anything
If flashing stock doesn’t help make a backup of current bios or bios- region with fpt
Tools: See Section C2 in
Intel (Converged Security) Management Engine: Drivers, Firmware and Tools
Look for ME System Tools v9.1 r7 - (2018-09-01) Should be ME 9.0 or 9.1 if I’m not mistaken.
Use Flash programming tool, fpt(w(64)), naming according to dos/ win/ win64 version.
fpt(w(64)) -d spi.bin would dump the complete chip, unclear if flash descriptor is unlocked already.
If you get an error use
fpt(w(64)) -bios -d biosreg.bin
Post ot attach the result
Don’t use these tools to write if you don’t have 1) a hardware programmer and 2) a valid backup of your complete spi chip!!!
I dont have any of those tools, btw even on device manager it shows as 12 cores, 6 physical cores and 6 virtual one…
Use fptw64 to dump your whole bios to see what’s going on? Personally would recommend you flash the latest official bios release and not an old one because the ME may not get updated to match the old version and you may encounter these weird symptoms.
Edit: Reach out to Ifb6 + Lost_N_Bios for help.
Edit: Read about one guy with similar issue who solved problem by removing cmos battery. Maybe worth a try.
Edit: Do not use EZ-Flash utility!
I did remove the battery CMOS but nothing changed, i tried flashing latest BIOS and even other versions but still have the same problem…
BTW i discovered something, when i disable hyperthreading i got 6 cores working, obviously without hyperthreading…When i enable hyperthreading it goes down 3 cores and 6 threads, it should be 6 cores and 12 threads.
I thing i might have done something wrong on UBU