Working with 64 bit operating systems, especially on client operating systems, still presents some challenges. One recent interesting effect I’ve run into is the redirection of the %windir%\System32 folder. When a 32 bit application attempts to access the folder, it is redirected to %windir%\SysWOW64, this allows those applications to use the correct version of various tools.
The difficulty comes in when trying to use certain tools, like bcdedit.exe, do not exist in the %windir%\SysWow64 directory and error out. The solution is to access the tools under the %windir%\SysNative folder which bypasses the redirection.
More information can be found here: http://msdn.microsoft.com/en-us/library/aa384187(VS.85).aspx
