You may be able to use BCDBoot to correct the BCD before rebooting. You can find more information about BCDBoot here: BCDboot Command-Line Options.
Basically, you would just add an "execute file" action into the template before rebooting and run bcdboot.exe C:\Windows (or whatever the path is to the Windows directory)
I'm assuming you use an ImageX image? Did you try to add a Partition action after deploying the Image with a Make Bootable action from the pulldown menu?