setupcomplete.cmd modification not working

I have modified the setupcomplete.cmd and I can't seem to get it to do anything but the first line of the command.  Does anyone know what I'm doing wrong?

%WINDIR%/setup/scripts/AltirisAgent.bat

if not exist C:\RISlog mkdir C:\RISlog
echo %date%,%time%,errorlevel: %errorlevel%,setupcomplete.CMD - 3: Begin >> c:\RISlog\deployment.log
%WINDIR%/setup/scripts/Agent.bat

It does run the altirisagent.bat file.  I'm testing the mkdir portion right now but I know it does not run the echo command and the command after.