I already explained this, but I'm going to detail it know so no more doubts about this.
When you install W8.1 EFI or W10 EFI, Microsoft signs your EFI firmware. It's a security measure, to detect modifications into your BootROM. This is done by a X509 certificate, Microsoft Windows Secure Boot Variable Signer, stored into one of the private parts of the NVRAM.
Code:
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The problem is, Microsoft is signing multiple times the BootROM. Most people have one signing certificate, some have two. I found three of those certificates into hardware dumps of two backplanes that couldn't boot anymore, read by SPI flash programmers after the SPI flash was removed from the board for repair.
I found two decent support article about the Secure Boot process,
Diving into Secure Boot and
Windows Secure Boot Key Creation and Management Guidance, but I still don't know when the signing is done and why is happening multiple times with Mac Pro 5,1.
So, if you have two of those, don't wait to Microsoft sign it again and cause havoc. Post here that you found two, I'll PM you with instructions.