Sorry for the delay in replying. My computer quit responding on the 18th and I had to reinstall Windows.
The switches are needed. For example, in RMDIR (remove directory), "/S" says to remove the directory tree (the directory itself and all files and sub-directories), and "/Q" implies quiet mode (do not query the user for permission to delete). The /R is necessary for the above reason, though not the /Q.
The paramaters used are as follows:
PROGRAMFILE = C:\Program Files
SYSTEMROOT = C:\Windows
You could try entering the commands manually at the command line, one by one, and see what happens, or try other commands like deltree or del. I hope you're able to get something to work.