If you need to create a .cmd that need to copy files in c:\windows\system32 there is an important thing to consider:
Remote pcs 32 or 64 bit O.S. version
Infact you need to consider this commands on 32 bits or 64 bits
if %PROCESSOR_ARCHITECTURE%==x86 (
copy file.dat %systemroot%\system32
) else (
copy file.dat %systemroot%\sysnative
)
infact, on 64 bit system command is interpreted like follow:
%systemroot%\system32 --> C:\Windows\SysWOW64
And check if you are using the 64 or 32 bit cmd.exe. (You did know there are two?)
The 32 bit one redirects system32 to SYSWOW64 - read the Wiki about wow64 at http://en.wikipedia.org/wiki/WoW64
64 bit... %windir%\system32\cmd.exe
32 bit... %windir%\syswow64\cmd.exe
in SCCM 2012 if cmd is executed like 32 bits you need to take care about this two options:
copy file_name %systemroot%\system32 (32 bit)
copy file_name %systemroot%\sysnative (64 bit)
Further details:
http://www.computerhope.com/forum/index.php?topic=127548.0