I have done this using an exec extension very successfully
This is the syntax:
SetOutPath $INSTDIR\${APPLICATION_DIR}
ExpandEnvStrings $0 %COMSPEC%
nsExec::ExecToStack '"C:\path-tobatch-file\commands.bat"'
Here is a link to the NSIS Wiki http://nsis.sourceforge.net/Docs/nsExec/nsExec.txt
DBQ
2010-07-16 13:19:45