I found a way to get server 2003 to work with BCDW on a forum:
http://www.msfn.org/board/index.php?showtopic=58410
Using the cracked_SETUPLDR_1_.BIN.zip that is on that website I have managed to get past the corrupted NTLDR error and boot into PE.
Only thing I am curious of is if there is a way to automatically replace the SETUPLDR.BIN with the cracked one from there website automatically?
