@d0minat0r
Have you tried the BIOS FlashBack? (Page 59.)
I have an X299 motherboard with a similar problem. No detectable ME module at all:
The Management Engine Interface is also missing from the Device Manager:
(Another system)
In my case, a simple BIOS update did not help. I have not tried FlashBack yet. However, I don’t have any boot related problems and I don’t understand what Intel ME has to do with boot.
Unfortunately I think this is a hardware failure that cannot be fixed in software. 