When running the install from the command prompt, I do use the entire path for -f1 and -f2. 


The .iss file, that I pasted above, has been reviewed, and they said there didn't look to be anything wrong with it.  I have also tried to create the .iss on multiple computers, with the same results after pushing out via command/script.  The silent install will only work on the machine, on which I created the .iss file.  If I try to push to a new computer, it immediately deletes all of the directories from the C:Program Files, except for the .admin directory. I will try to create the .iss file on a machine in our lab OU, since most of the computers that we push out to are in that same OU.