I would guess that its because the ECU hasnt gone into bootmode. Also, you dont need to be in bootmode to read the eeprom, I would try reading over ODB to check your cable etc is working. What tool are you using? I use argdubs tool and havent had any issues.
It was not reading in OBD or in Bootmode.
Solved it though.
Had to move/lift of the SMD resistors on the board and I was able to read and rewrite the updated EEPROM. resoldered the risitor and now all works.