redrider1940 is right, it could be down to an issue with your source machine. I've also seen this from "clean" images. If you run bcdedit in Windows it will return details of the boot manager and boot loader. Since you are seeing two boot loaders you need to make a note of the duplicate identifier value (usually something like this {cf21078c-6cd0-11e2-ab54-dc36a25fd8ae} ) then as you are already downloading bcdedit.exe to WinPE (see REMEXEC35 in your script), you can add a new line to run bcdedit.exe /delete {cf21078c-6cd0-11e2-ab54-dc36a25fd8ae} to do away with the additional entry. I'd run it after line 41 once BCDboot has been run Windows will then load as normal. Its a workaround, but it should get you to where you want to be.
Hope that helps 
Martyn Ayers
MarXtar Ltd/MarXtar Corporation
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