Comment 4 for bug 468664

hmm strange, the relevant code is

 bcdedit = join_path(os.getenv('SystemDrive'), 'bcdedit.exe')
if not os.path.isfile(bcdedit):
     bcdedit = join_path(os.environ['systemroot'], 'sysnative', 'bcdedit.exe')
if not os.path.isfile(bcdedit):
     bcdedit = join_path(os.environ['systemroot'], 'System32', 'bcdedit.exe')
if not os.path.isfile(bcdedit):
     log.error("Cannot find bcdedit")

So you would only use sysnative only if there is a file C:\Windows\sysnative\bcdedit.exe, otherwise it will try C:\Windows\System32\bcdedit.exe
Are you sure that there is no file called C:\Windows\sysnative\bcdedit.exe?