VF50 Production programming CE6 to CE7

We are using the VF50 with CE7.
The new modules come installed with CE6 so need to be updated.
I have updated 1 and configured it to run our application, then backed up the
Configblock , registry and filesystem.

I have then create a production programming USB stick to configure new boards.

The problem i have:
If I try to get the batch file to update everything on one go, after a reboot the OS fails to boot.
The only way I can recover this then be recovered by using the SD card and serial console recovery.

The current working method requires 2 USB sticks:
1st USB stick updates eboot.img and nk7.bin
then after a reboot
2nd USB stick updates configblock,registry and filesystem.
This works fine, but i’m unsure why?

Below is the batch file i have tried to use to do the process in one go.
Should i be able to update everything in one go?
Jamie.

ProductionProgramming.bat

@ECHO OFF

REM ################################################################################
REM Configuration Section

REM Path to UpdateTool.exe (relatvie to this batch file)
set PATH_UPDATETOOL=\USB HD\UpdateTool

REM Configuration Section end
REM ################################################################################

ECHO Toradex Production Programming
ECHO ******************************
REM First clear registry
“%PATH_UPDATETOOL%\updatetool.exe” /cu
REM Update bootloader
“%PATH_UPDATETOOL%\updatetool.exe” /u bootloader,raw,\USB HD\backup\eboot.img
REM Update image
“%PATH_UPDATETOOL%\updatetool.exe” /u os,bin,\USB HD\backup\nk7.bin
REM Update Config block
“%PATH_UPDATETOOL%\updatetool.exe” /u configblock,raw,\USB HD\backup\Backup.cfg
REM Update Registry
“%PATH_UPDATETOOL%\updatetool.exe” /u registry,raw,\USB HD\backup\Backup.ivr
REM Update File System
“%PATH_UPDATETOOL%\updatetool.exe” /u filesystem,raw,\USB HD\backup\Backup.ivf
ECHO Production programming done.
ECHO *******************************