QUOTE
When I ran the /s it looked like the computer was doing something, then it just stopped, and the system was the same as before.
I think I know what's happening. The installation starts silently, but it can't locate the setup.iss which halts the process. You're installer is an sfx, which extracts it's files to the %temp% folder. Like I said before, try right-clicking the installer and extract it's files to a folder using WinRAR. Then copy your setup.iss to that folder and run the setup there with /s switch.
However, there are compiled exes which you can't extract the files. In that case, this is what I normally do.
1. I create an sfx for my setup.iss that will extract it silently to the root of my drive c
2. I create a batch file that has this code.
CODE
start /w setup1.exe
start /w setup.exe /s /f1"c:\setup.iss"
del c:\setup.iss
*Note: the setup1.exe is the sfx for my setup.iss