As mentioned here and here, bootrec.exe and bcdedit.exe have trouble functioning from a usb-booted WinPE environment. They tend to see the wrong sets of files and they also tend to break things (which I found out the hard way). As of yet, I have found no way to get them to see any file set other than that from which they were booted, IE not the WinPE environment. Booted from an actual disk, they work fine. It seems to be an issue with usb drivers in windows PE & RE from what little I was able...
