The VIN, along with other data that must remain permanently in the ECM when power is switched off is stored in the NVRAM (non volatile RAM) area of the flash memory.
That memory is made up of two banks of flash memory, so that a backup copy can be maintained. The backup is needed in case power is removed while the ECM is erasing/updating the data. One bank will always contain valid data - even if the other one has been erased.
EFILive makes an "educated" guess as to which bank contains the current/valid data. It could be that EFILive picked the wrong bank.

If you read out a few of the TCMs and send me the tune files, I can convert them to bin files and can investigate the data in the NVRAM area to see if it is viable or not.
Also send me a screen shot of the [F4: OBD] data for each TCM before you read it out.

Send then to paul@efilive.com

Regards
Paul