Not really "expected/ok".
The $FE reply code is an internal code from the boot loader (running in the PCM) to the EFILive software telling the software that the check sum in the PCM is incorrect. When loading a COS operating system the check sum is deliberately left incorrect to prevent any attempt to operate the vehicle until a valid calibration is flashed. So yes, it is expected but no it should not be displayed to the user as an error. It should be handled silently by the software and a message such as "You should now program the calibrations" should be displayed to the user instead.
I'm, working on fixing it for the next update.
Regards
Paul