Da ajuda do CMD.EXE:
CMD [/A | /U] [/Q] [/D] [/E:ON | /E:OFF] [/F:ON | /F:OFF] [/V:ON | /V:OFF]
[[/S] [/C | /K] string]
...
/D Disable execution of AutoRun commands from registry (see below)
...
If /D was NOT specified on the command line, then when CMD.EXE starts, it
looks for the following REG_SZ/REG_EXPAND_SZ registry variables, and if
either or both are present, they are executed first.
HKEY_LOCAL_MACHINE\Software\Microsoft\Command Processor\AutoRun
and/or
HKEY_CURRENT_USER\Software\Microsoft\Command Processor\AutoRun
Então você deve ser capaz de criar a entrada de registro com um comando para iniciar seu programa.